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  -----------------------------------------------------------------------
  Document             
  Identification       
  -------------------- --------------------------------------------------
  **Document Title**   User's Manual (UM) for PatentIn 3.5

  **CDRL**             PTO-SP-03

  **USPTO Contract**   DOC50PAPT0501005

  **Task Order Title** PatentIn 3.5

  **Task Order Type**  Discrete

  **Task Order         CSCS-07-61
  Number**             
  -----------------------------------------------------------------------

Version Control Log

  ---------------------------------------------------------------------------
  Version    Date Change  Nature of Change       Pages Affected   Signature
  Control    Effective                                            Authority
  Number                                                          
  ---------- ------------ ---------------------- ---------------- -----------
  N/A        11/10/98     Initial document       All              J. Paccassi
                          prepared by Lockheed                    
                          Martin Corporation                      

  Draft 1.0  06/03/99     Initial document       All              J. Paccassi
                          prepared by CSC                         

  Version    09/16/99     Incorporate USPTO      i, ii, 1v, 3-5,  J. Paccassi
  1.0                     comments and updates   3-6, 4-2, 4-3,   
                          from Functional        4-5,\            
                          Qualification Test     4-6, 5-2, 5-3,\  
                          (FQT)                  5-5, 6-2, 6-4,\  
                                                 6-7, 7-2, 7-3,\  
                                                 8-3 through 8-9  

  Version    06/02/00     Update document to     All              J. Paccassi
  1.1                     reflect change from                     
                          JAVA to C++                             

  Version    06/22/00     Incorporate USPTO      3-5, 3-10, 5-4,  J. Paccassi
  1.2                     updates from FQT       5-10, 6-2, 8-4   

  Version    01/26/01     PatentIn 3.1 release   All              J. Paccassi
  2.0                                                             

  Version    04/27/01     Updates to PatentIn    All              J. Paccassi
  2.1                     3.1 release                             

  Version    10/16/03     Updates to PatentIn    All              J. Paccassi
  2.2                     3.2 release                             

  Version    03/18/04     Updates to PatentIn    All              J. Paccassi
  2.3                     3.3 release                             

  Version    07/30/04     Updates to PatentIn    5-16             S. Babil
  2.4                     3.3 release                             

  Version    06/14/06     Updates to PatentIn    All              S. Babil
  2.5                     3.4 release                             

  Version    10/09/2007   Updates to PatentIn    All              S. Babil
  2.6                     3.5 release                             
  ---------------------------------------------------------------------------

Executive Summary

This User's Manual (UM) does not conform to the Data Item Description
(DID) for the UM, PTO-SP-03. Instead, as required by Section 2.4.4.6 of
the Web PatentIn (WPI) Task Management Plan (TM02) version 1.11, it is
being updated using the format in which the document was originally
prepared.

This UM is being updated at United States Patent and Trademark Office's
(USPTO's) direction under task order number CSCS-07-61 to include
changes for PatentIn 3.5.

Table of Contents

[**Section 1** **Introduction 1-2**](#introduction)

[1.1 Purpose 1-2](#purpose)

[1.2 Conventions 1-2](#conventions)

[1.3 Overview 1-2](#overview)

[Section 2 System Requirements and PatentIn 3.5 Access
2-1](#system-requirements-and-patentin-3.5-access)

[2.1 System Requirements 2-1](#system-requirements)

[2.2 PatentIn Access 2-1](#patentin-access)

[Section 3 Getting Started 3-1](#getting-started)

[3.1 Sequence Screen 3-1](#sequence-screen)

[3.2 Project Menu 3-1](#project-menu)

[3.3 Creating and Saving a New Project
3-2](#creating-and-saving-a-new-project)

[3.4 Opening a Project 3-3](#opening-a-project)

[3.5 Saving a Project 3-4](#saving-a-project)

[3.6 Viewing a Work File 3-5](#viewing-a-work-file)

[3.7 Viewing Work in Progress 3-6](#viewing-work-in-progress)

[3.8 View a Sequence Listing 3-6](#view-a-sequence-listing)

[3.9 Viewing Error Reports 3-8](#viewing-error-reports)

[3.10 Rename Sequence 3-8](#rename-sequence)

[3.11 Exit PatentIn 3-9](#exit-patentin)

[3.12 How to Use Online Help 3-9](#how-to-use-online-help)

[3.13 Message Dialog 3-10](#message-dialog)

[Section 4 Project and Application Data
4-1](#project-and-application-data)

[4.1 Application Steps Menu 4-1](#application-steps-menu)

[4.2 Project Data 4-1](#project-data)

[4.3 Prior Application Information 4-2](#prior-application-information)

[4.4 Applicant Data 4-4](#applicant-data)

[4.4.1 Individual Applicants 4-4](#individual-applicants)

[4.4.2 Organization Applicants 4-6](#organization-applicants)

[Section 5 Sequence Data 5-1](#sequence-data)

[5.1 Sequence 5-1](#sequence)

[5.1.1 Selecting a Standard Organism
5-2](#selecting-a-standard-organism)

[5.1.2 Creating Default Explanations for \"n"s and \"Xaa"s
5-2](#creating-default-explanations-for-ns-and-xaas)

[5.1.3 Searching for a Sequence 5-3](#searching-for-a-sequence)

[5.1.4 Clearing the Screen 5-3](#clearing-the-screen)

[5.2 Adding a Sequence 5-3](#adding-a-sequence)

[5.3 Importing a Sequence 5-4](#importing-a-sequence)

[5.3.1 Format for Multi-Sequence Data Files (Non-ST.25 Sequence Listing
File) to be Imported by PatentIn 3.5
5-5](#format-for-multi-sequence-data-files-non-st.25-sequence-listing-file-to-be-imported-by-patentin-3.5)

[5.3.2 Format for Single Sequence Data Files to be Imported by PatentIn
3.5
5-6](#format-for-single-sequence-data-files-to-be-imported-by-patentin-3.5)

[5.3.3 Importing Sequences from a Project
5-7](#importing-sequences-from-a-project)

[5.3.4 Importing Sequences from a PatentIn Generated ST.25 Sequence
Listing File
5-8](#importing-sequences-from-a-patentin-generated-st.25-sequence-listing-file)

[5.4 Copying a Sequence 5-14](#copying-a-sequence)

[5.5 Pasting a Sequence 5-14](#pasting-a-sequence)

[5.6 Deleting a Sequence 5-15](#deleting-a-sequence)

[5.7 Skip a Sequence 5-15](#skip-a-sequence)

[5.8 Restoring a Sequence 5-15](#restoring-a-sequence)

[5.9 Reordering Sequences 5-16](#reordering-sequences)

[5.10 Changing a Sequence Type 5-18](#changing-a-sequence-type)

[5.11 Validating Sequences 5-18](#validating-sequences)

[5.12 Saving Sequences 5-19](#saving-sequences)

[5.13 Reloading a Saved Project 5-19](#reloading-a-saved-project)

[5.14 Adding Custom Codons 5-19](#adding-custom-codons)

[5.15 Adding a Custom Organism 5-20](#adding-a-custom-organism)

[5.16 Artificial Sequence or Unknown Organism
5-22](#artificial-sequence-or-unknown-organism)

[Section 6 Feature Data 6-1](#feature-data)

[6.1 Sequence Features 6-1](#sequence-features)

[6.1.1 Feature Key Selection 6-2](#feature-key-selection)

[6.1.2 Additional Information Required for Modified_Base
6-3](#additional-information-required-for-modified_base)

[6.1.3 Additional Information on CDS (Coding Sequence)
6-4](#additional-information-on-cds-coding-sequence)

[6.1.4 Further Definition of "N" or "Xaa"
6-4](#further-definition-of-n-or-xaa)

[6.1.5 Selecting an Amino Acid 6-5](#selecting-an-amino-acid)

[6.1.6 Additional Information for MOD_RES
6-6](#additional-information-for-mod_res)

[Section 7 Publication Data 7-1](#publication-data)

[7.1 Publication Type Screen 7-1](#publication-type-screen)

[7.2 Journals Publication Information
7-2](#journals-publication-information)

[7.3 Databases Publication Information
7-3](#databases-publication-information)

[7.4 Patents Publications Information
7-4](#patents-publications-information)

[7.5 Theses Publication Information
7-5](#theses-publication-information)

[Section 8 Creating a Sequence Listing Project File
8-1](#creating-a-sequence-listing-project-file)

[8.1 Sequence Listing File 8-1](#sequence-listing-file)

[8.2 Generating a Sequence Listing File
8-1](#generating-a-sequence-listing-file)

[8.3 Viewing a Sequence Listing File
8-2](#viewing-a-sequence-listing-file)

[8.4 Copying the Sequence Listing to a Disk
8-3](#copying-the-sequence-listing-to-a-disk)

[Section 9 List of Acronyms 9-1](#list-of-acronyms)

[Appendix A Field Identifiers, Lengths and Types
A-1](#field-identifiers-lengths-and-types)

[Appendix B Country Codes B-1](#country-codes)

[Appendix C Conversion Table Between Nucleotide Triplets (Codons) and
One- and Three Letter Amino Acid Codes
C-1](#conversion-table-between-nucleotide-triplets-codons-and-one--and-three-letter-amino-acid-codes)

[Appendix D Nucleotide Sequence Features
D-1](#nucleotide-sequence-features)

[Appendix E Amino Acid Sequence Features
E-1](#amino-acid-sequence-features)

[Appendix F Data Tables for Mod_Res Sequence Features
F-1](#data-tables-for-mod_res-sequence-features)

[Appendix G Additional Lipid Sequence Features
G-1](#additional-lipid-sequence-features)

[Appendix H Acceptable Characters In The Sequence Description Field
H-1](#acceptable-characters-in-the-sequence-description-field)

[Appendix I Additional Modified_Base Sequence Features
I-1](#additional-modified_base-sequence-features)

[Appendix J Technical Notes J-1](#technical-notes)

[J.1 Microsoft® Access Notes J-1](#microsoft-access-notes)

[J.1.1 Installing Microsoft® Access 97
J-1](#installing-microsoft-access-97)

[J.1.2 Hints and Tips J-1](#hints-and-tips)

[J.2 General Hints and Tips J-2](#general-hints-and-tips)

[J.3 Installation and Testing Notes
J-2](#installation-and-testing-notes)

[J.3.1 PatentIn Installation and Repair
J-2](#patentin-installation-and-repair)

[J.3.2 Testing Configurations J-3](#testing-configurations)

[J.3.3 Internet Explorer Considerations
J-4](#internet-explorer-considerations)

**List of Figures**

[Figure 3‑1: Sequence Screen 3-1](#_Ref480778919)

[Figure 3‑2: Project Menu 3-2](#_Ref479749728)

[Figure 3‑3: Save As Screen 3-3](#__RefHeading___Toc178405772)

[Figure 3‑4: Open Screen 3-4](#__RefHeading___Toc178405773)

[Figure 3‑5: Save As Screen 3-5](#__RefHeading___Toc178405774)

[Figure 3‑6: View Work in Progress Window
3-6](#__RefHeading___Toc178405775)

[Figure 3‑7: View Sequence Listing Window
3-7](#__RefHeading___Toc178405776)

[Figure 3‑8: View Error Report Window 3-8](#__RefHeading___Toc178405777)

[Figure 3‑9: Rename Sequence Screen 3-8](#_Ref137364021)

[Figure 3‑10: Exit PatentIn Screen 3-9](#_Ref137364049)

[Figure 3‑11: Help Screen 3-9](#_Ref137364070)

[Figure 3‑12: Message Dialog Screen 3-10](#_Ref137364151)

[Figure 4‑1: Application Steps Menu 4-1](#__RefHeading___Toc178405782)

[Figure 4‑2: Project Data Screen 4-2](#__RefHeading___Toc178405783)

[Figure 4‑3: Prior Application Information Screen 4-3](#_Ref137364286)

[Figure 4‑4: Application Data Screen 4-4](#_Ref137440674)

[Figure 4‑5: Individual Applicants Screen
4-5](#__RefHeading___Toc178405786)

[Figure 4‑6: Organization Applicants Screen
4-6](#__RefHeading___Toc178405787)

[Figure 5‑1: Sequence Screen 5-1](#__RefHeading___Toc178405788)

[Figure 5‑2: Selecting an Organism Screen
5-2](#__RefHeading___Toc178405789)

[Figure 5‑3: Add a Sequence Screen 5-3](#__RefHeading___Toc178405790)

[Figure 5‑4: Import Sequence(s) Screen
5-4](#__RefHeading___Toc178405791)

[Figure 5‑5: Sample ASCII Sequence Data
5-6](#__RefHeading___Toc178405792)

[Figure 5‑6: Sequence Type Selection Screen
5-6](#__RefHeading___Toc178405793)

[Figure 5‑7: Sequences Being Imported Screen
5-7](#__RefHeading___Toc178405794)

[Figure 5‑8: Validation Errors Screen 5-7](#__RefHeading___Toc178405795)

[Figure 5‑9: Select Sequences From Project Screen
5-8](#__RefHeading___Toc178405796)

[Figure 5‑10: Import to New Project Message Dialog Screen
5-9](#__RefHeading___Toc178405797)

[Figure 5‑11: Save Project Screen 5-9](#__RefHeading___Toc178405798)

[Figure 5‑12: Parsing Applicant Names Screen
5-10](#__RefHeading___Toc178405799)

[Figure 5‑13: Added All Names Message Dialog Screen
5-11](#__RefHeading___Toc178405800)

[Figure 5‑14: The Skipped Sequence Type Selection Screen
5-12](#__RefHeading___Toc178405801)

[Figure 5‑15: Invalid Sequence Type Encountered Screen
5-12](#__RefHeading___Toc178405802)

[Figure 5‑16: Select Sequences to Import Screen
5-13](#__RefHeading___Toc178405803)

[Figure 5‑17: Edit Menu 5-14](#__RefHeading___Toc178405804)

[Figure 5‑18: Sequence Recovery Screen
5-16](#__RefHeading___Toc178405805)

[Figure 5‑19: Reorder Sequences Screen
5-17](#__RefHeading___Toc178405806)

[Figure 5‑20: Change Sequence Type Screen
5-18](#__RefHeading___Toc178405807)

[Figure 5‑21: Custom Codons Input Screen
5-19](#__RefHeading___Toc178405808)

[Figure 5‑22: Amino Acid Drop Down List Screen
5-20](#__RefHeading___Toc178405809)

[Figure 5‑23: Custom Organism Input Screen
5-21](#__RefHeading___Toc178405810)

[Figure 5‑24: Artificial Sequence/Unknown Organism Comment
5-22](#__RefHeading___Toc178405811)

[Figure 6‑1: Features Screen 6-1](#__RefHeading___Toc178405812)

[Figure 6‑2: Feature Names/Key Selection Screen
6-3](#__RefHeading___Toc178405813)

[Figure 6‑3: Feature Names/Key Selection Screen with Modified Base
6-4](#_Ref501932744)

[Figure 6‑4: Feature Names/Key Selection Screen with LIPID Selected
6-5](#__RefHeading___Toc178405815)

[Figure 6‑5: Feature Names/Key Selection Screen with MOD_RES Selected
6-6](#__RefHeading___Toc178405816)

[Figure 6‑6: First MOD_RES Pull Down List
6-7](#__RefHeading___Toc178405817)

[Figure 6‑7: Second MOD_RES Pull Down List
6-8](#__RefHeading___Toc178405818)

[Figure 7‑1: Publication Type Screen 7-1](#__RefHeading___Toc178405819)

[Figure 7‑2: Journals Publication Information Screen
7-2](#_Ref476978663)

[Figure 7‑3: Databases Publication Information Screen
7-3](#__RefHeading___Toc178405821)

[Figure 7‑4: Patents Publication Information Screen
7-4](#__RefHeading___Toc178405822)

[Figure 7‑5: Theses Publications Information Screen
7-5](#__RefHeading___Toc178405823)

[Figure 8‑1: Sequence Generation Screen
8-1](#__RefHeading___Toc178405824)

[Figure 8‑2: Second Sequence Generation Screen
8-2](#__RefHeading___Toc178405825)

[Figure 8‑3: View Results Window 8-2](#__RefHeading___Toc178405826)

[Figure 8‑4: Copy to Disk Screen 8-3](#__RefHeading___Toc178405827)

[Figure J‑1: PatentIn Repair and Uninstall
J-3](#__RefHeading___Toc137961134)

List of Tables

[Table 1‑1: Document Conventions 1-2](#__RefHeading___Toc178405828)

[Table 5‑1: Header for Sequence 5-5](#__RefHeading___Toc178405829)

[Table 9‑1: Acronyms 9-1](#__RefHeading___Toc178405830)

[Table A‑1: Field Name, Identifier, Size, and Type
A-1](#__RefHeading___Toc178405831)

[Table B‑1: Country Codes B-1](#__RefHeading___Toc178405832)

[Table C‑1: Exchange Nucleotide Characters and Amino Characters
C-1](#__RefHeading___Toc178405833)

[Table D‑1: Nucleotide Sequence Features
D-1](#__RefHeading___Toc178405834)

[Table E‑1: Amino Acid Sequence Features
E-1](#__RefHeading___Toc178405835)

[Table F‑1: First Data Table for MOD_RES Sequence Features
F-1](#__RefHeading___Toc178405836)

[Table F‑2: Second Data Table for MOD_RES Sequences
F-1](#__RefHeading___Toc178405837)

[Table G‑1: Additional Lipid Sequence Features
G-1](#__RefHeading___Toc178405838)

[Table H‑1: Acceptable Characters in the Sequence Description Field
H-1](#__RefHeading___Toc178405839)

[Table I‑1: Modified_base Sequence Features
I-1](#__RefHeading___Toc178405840)

# Introduction 

## Purpose

PatentIn facilitates the creation of sequence listings for inclusion in
patent applications sequences. It accepts data about the sequences
validates the data, creates a sequence listing file and a mechanism for
printing out and saving to removable medium for submission. This manual
describes how to use PatentIn.

## Conventions

Consistent visual cues and standard keyboard operations are used
throughout this manual. These conventions are listed in Table 1-1.

[]{#__RefHeading___Toc178405828 .anchor}Table 1‑1: Document Conventions

  ----------------------------------------------------------------------------
  **Notation**   **Represents**               **Example**
  -------------- ---------------------------- --------------------------------
  **Bold** type  Name of a function, file,    Click on **Exit**.
                 menu item, or programming    
                 construct.                   

  ----------------------------------------------------------------------------

## Overview

PatentIn is a computer program designed to expedite the preparation of
United States Patent and Trademark Office (USPTO) patent applications
containing nucleic acid and polypeptide sequences.

PatentIn complies with all format requirements specified in World
Intellectual Property Organization Standard (WIPO) ST.25 and the related
United States (US) final rule, \"Requirements for Patent Applications
Containing Nucleotide Sequence or Amino Acid Disclosures.\" The
application runs on Windows XP/Windows Vista and the screen displays are
in English. Since the sequence listings generated by PatentIn comply
with the ST.25, this program has worldwide applicability.

For ease of use, the design follows the standard Windows user interface
conventions.

PatentIn includes the following tools:

-   **A Sequence Editor**\
    The primary tool within PatentIn is the sequence editor, which
    enables you to enter and modify both nucleic acid and protein
    sequence listings, as well as import PatentIn generated ST.25
    sequence listing files or sequence data files created by another
    editor or word processor (provided they are stored as American
    Standard Code for Information Interchange (ASCII) text files).

    When working in PatentIn you may enter data in any order, and also
    add, remove, or revise sequence listing data at any time. You may
    also save a partially completed project and finish it at a later
    time. PatentIn does not require that a project exist or remain on a
    particular machine or device. Users are free to e-mail files to
    clients or each other so that they might review/update them.

-   **A Sequence Generator**\
    After you have entered all the data necessary for your patent
    application, PatentIn enables you to generate your application. The
    application consists of a computer-readable, ST.25 compliant file
    containing a sequence listing file.

# System Requirements and PatentIn 3.5 Access

## System Requirements

PatentIn is a self-contained application that can be downloaded from the
USPTO website. It operates in a Windows XP and Windows Vista
environment. A minimum of 512 Megabytes (MBs) of memory is required.
Additional memory may be required for large patent applications. For the
best performance 1 Gigabytes (GBs) of memory is recommended for very
large projects, projects with 100,000 sequences or a sequence
approaching 12 MB. The disk space required to install PatentIn 3.5 is
about 6.5 MBs. Additional disk space is required to store project files
and sequence listing files.

For PatentIn to work correctly, the "TMP" environment variable must
point to a valid directory, and the "PATH" environment variable must
include the Disc Operating System (DOS) backup command in the path. Most
Windows installations will meet these requirements.

**Special Note for users with very large sequences and large numbers of
sequences**: USPTO has located a viewer that works for very large text
files. A 60 day evaluation version is downloadable at
[www.fileviewer.com/](http://www.uspto.gov/cgi-bin/exitconf/internet_exitconf.pl?target=www.fileviewer.com/).
The viewer is named \"V\" and the version is 2000 SR-1. USPTO was able
to successfully open files of 60 MB and 120 MB using an earlier version
of the V software and the viewer was tested on a laptop with Windows 98.
(LocalAdmin may be required for installation.)

## PatentIn Access

PatentIn was designed for installation on individual computers. It can
be downloaded onto your Personal Computer (PC) and, if desired, the
project files can be stored remotely. The program can be downloaded from
the USPTO web page,
<http://www.uspto.gov/web/offices/pac/patin/patentinrel.htm>. Before the
installation of PatentIn 3.5, be sure to close all running applications
on your computer and then follow the instructions found on the Web page
to download PatentIn 3.5 and install it on your PC. Upon completing the
installation, an icon will be placed on your desktop. Access to the
PatentIn 3.5 application program occurs when you double-click on the
PatentIn 3.5 icon.

# Getting Started

## Sequence Screen

When you first access PatentIn by double-clicking on the PatentIn 3.5
icon on your desktop, you have immediate access to the Sequence Screen.

The Sequence Screen (Figure 3-1) is the main screen.

![](media/image3.png){width="6.247916666666667in"
height="4.763194444444444in"}[]{#_Ref480778919 .anchor}

Figure 3‑1: Sequence Screen

The Sequence Screen (Figure 3-1) provides the user with five drop-down
menus, three of which provide access to the real-time system interface.
They are Project, Application Steps, and Help. The remaining two
drop-down menus, Edit and View, are general Microsoft (MS) Windows-type
menus. The user may select any one of the three drop-down menus when a
project is started. PatentIn presents an empty project upon startup
entitled "Untitled." The user can open an existing project with the
Project Menu (Figure 3-2).

## Project Menu

The Project Menu (Figure 3-2) enables you to create and save a project.
Selecting "**Save**" displays the Save As Screen (Figure 3-5) where a
new project file is created and saved. Selecting "**Open**" displays the
Open Screen (Figure 3-4) where the user can select a previously saved
project to open. The "Exit PatentIn" selection closes the application.
Menu items that require a project to be opened, or an output file to be
present, are grayed out until those conditions are met.

The Project Menu selections are shown in Figure 3-2. The user will see a
list of selectable Menu Items under the Project menu and the active
project name on the upper left-hand corner of the screen. In this case,
Untitled is shown as no project has yet been opened or saved.

![](media/image4.png){width="6.497222222222222in"
height="4.959027777777778in"}[]{#_Ref479749728 .anchor}

Figure 3‑2: Project Menu

## Creating and Saving a New Project

**To create and save a new project,** begin building the new file upon
opening the main screen, Sequence Screen, or perform the following
steps:

1.  Select **New** from the Project Menu. This clears the all of the
    current project information.

2.  Select Save from the Project Menu. The Save As Screen (Figure 3-3)
    appears.

3.  Enter the new file name into the **File Name** dialog box in a
    desired folder.

4.  Click on **Save** to create the new file.

5.  The name for the new project will be displayed on the upper
    left-hand corner of the screen.

![](media/image5.png){width="5.84375in" height="4.34375in"}

[]{#__RefHeading___Toc178405772 .anchor}Figure 3‑3: Save As Screen

**Note**[:]{.smallcaps} Both **Save** and **Save As** save only the
project (\*.prj) file. The generated listing is saved as a text file
when the project is generated.

## Opening a Project

**To open an existing project:**

1.  Select **Open** from the **Project** menu. The Open Screen (Figure
    3-4) appears.

```{=html}
<!-- -->
```
6.  Open the directory where the file is located.

7.  Double-click on the file name to open the file.

8.  You are returned to the main screen. The name of the opened project
    is displayed in the upper left-hand corner of the PatentIn screen,
    indicating the project is active.

![](media/image6.png){width="5.84375in" height="4.34375in"}

[]{#__RefHeading___Toc178405773 .anchor}Figure 3‑4: Open Screen

**Special Note** for users with very large sequences or large numbers of
sequences: It takes some time for a large project to clear from memory.
This is especially noticed when immediately reopening the project.

## Saving a Project

**To save a project:**

When a project is saved for the first time, the user is automatically
prompted to enter a file name.

1.  Select **Save** from the **Project** menu. The Save As Screen(Figure
    3-5) will appear if the project has not previously been named.
    Otherwise, the project will be saved as the previously opened or
    created name.

2.  Select the directory where you want to save the file.

3.  Type the new file name in the **File Name** dialog box.

4.  Click on the **Save** button to save the project with the new file
    name.

5.  PatentIn returns you to the main screen. The new name is displayed
    in the upper left-hand corner of the screen, indicating that the
    project is active.

**To save under a different file name:**

1.  Select **Save As** from the **Project** menu. The Save As Screen
    (Figure 3-5) will appear.

```{=html}
<!-- -->
```
9.  Select the directory where you want to save the file.

10. Type the new file name in the **File Name** dialog box.

11. Click on the **Save** button to save the project with the new file
    name.

12. PatentIn returns you to the main screen. The new name is displayed
    in the upper left-hand corner of the screen, indicating that the
    project is active.

![](media/image7.png){width="4.855555555555555in"
height="3.604861111111111in"}

[]{#__RefHeading___Toc178405774 .anchor}Figure 3‑5: Save As Screen

## Viewing a Work File

The user can view the current work in progress by creating a work file.
This work file provides a vehicle for the user to view the data for the
entire project in a single place instead of reviewing each individual
screen. Use caution not to confuse the work file with the sequence
listing.

**To see the work file:**

From the Project Menu, select **View/Print Work In Progress**.

## Viewing Work in Progress

PatentIn provides the user with an on-screen display of the Patent
Application with the, as shown in Figure 3-6. The name of the work file
is the name of the current PatentIn project followed by
"\_WorkFile.txt."

![](media/image8.png){width="6.15625in" height="4.020833333333333in"}

[]{#__RefHeading___Toc178405775 .anchor}Figure 3‑6: View Work in
Progress Window

**To view the current patent application:**

1.  From the Project menu, select **View/Print** **Work In Progress**.

```{=html}
<!-- -->
```
13. To print the report, click on **File** then **Print**.

14. To exit the screen, click on **File** then **Exit**.

## View a Sequence Listing

PatentIn provides the user with an on-screen view of the Sequence
Listing with the, as shown in Figure 3-7. The name of the generated
listing is the name of the current PatentIn project followed by
"\_ST25.txt."

![](media/image9.png){width="6.5in" height="4.40625in"}

[]{#__RefHeading___Toc178405776 .anchor}Figure 3‑7: View Sequence
Listing Window

**To view the sequence listing:**

1.  From the Project menu, select **View/Print Sequence Listing**.

```{=html}
<!-- -->
```
15. To print the report, click on **File** then **Print**.

16. To exit the screen, click on **File** then **Exit**.

**Note**[:]{.smallcaps} The sequence must first be generated.

## Viewing Error Reports

PatentIn provides the user with an on-screen Error Report with the
Figure 3-8, if one exists, for the opened project. The name of the error
log file is the name of the current PatentIn project followed by
"\_ErrorLog.txt."

![](media/image10.png){width="6.510416666666667in" height="3.09375in"}

[]{#__RefHeading___Toc178405777 .anchor}Figure 3‑8: View Error Report
Window

**To view an error report:**

1.  From the Project menu, select View/Print Error Report.

```{=html}
<!-- -->
```
17. To print the error report, click on the **File** then **Print**.

18. To exit the screen, click on **File** then **Exit**.

## Rename Sequence

A new feature of PatentIn is the ability to change the name of a
sequence, as shown in Figure 3-9.

![](media/image11.png){width="2.96875in"
height="1.9375in"}[]{#_Ref137364021 .anchor}

Figure 3‑9: Rename Sequence Screen

1.  To open the **Rename Sequence** screen, click on the Sequence Name.

2.  From the Project Menu,select **Rename Sequence**.

3.  Type the new sequence name in the **Rename Sequence** dialog box.

4.  Click on the **OK** button.

## Exit PatentIn

If the project does not have a current save, the user will be queried
with the about whether the project should be saved, as shown in Figure
3-10.

![](media/image12.png){width="2.7708333333333335in"
height="1.3125in"}[]{#_Ref137364049 .anchor}

Figure 3‑10: Exit PatentIn Screen

## How to Use Online Help

Online help is available for most of the PatentIn screens. Figure 3-11,
presents a typical help screen retrieved by pressing F1 or the help
button. This example is the help screen access from the Sequence Screen.
To exit the **Help** screen, click on the **OK** button to close
caption.

![](media/image13.png){width="5.958333333333333in"
height="4.697916666666667in"}[]{#_Ref137364070 .anchor}

Figure 3‑11: Help Screen

## Message Dialog 

The Figure 3-12 is a screen that appears if one of the action buttons
(Add, for example, described in Section 4, Project, and Applicant Data)
is pressed and an entry has not been made to the input area of the
screen.

![](media/image14.png){width="2.4895833333333335in"
height="1.3125in"}[]{#_Ref137364151 .anchor}

Figure 3‑12: Message Dialog Screen

# Project and Application Data

Once the Sequence Listing data file has been created, the user can add
information to the application.

## Application Steps Menu

The Application Steps Menu (Figure 4-13) selections are available when a
project is started. The project name is visible at the upper left corner
of the screen. In this example the user has opened an existing project
called New Name.

![](media/image15.png){width="6.247916666666667in" height="4.76875in"}

[]{#__RefHeading___Toc178405782 .anchor}Figure 4‑13: Application Steps
Menu

## Project Data

The Project Data Screen (Figure 4-14) provides the user with input
fields to establish the identifying information for the new invention.
This information is the key that establishes the title of the invention
and the filing date.

**Note**[:]{.smallcaps} The mandatory information fields (Title of
Invention and Application File Reference) are in red and marked with
asterisks.

![](media/image16.png){width="6.427083333333333in"
height="3.8020833333333335in"}

[]{#__RefHeading___Toc178405783 .anchor}Figure 4‑14: Project Data Screen

**To enter project data:**

1.  Enter the **Title Of Invention**. This information is mandatory.

```{=html}
<!-- -->
```
19. Enter the **Current Application Number**, if one exists. If an
    application is entered, the current filing date becomes mandatory.

20. Enter the **Current Filing Date**. The date format is numeric:
    YYYY-MM-DD.

21. Enter the **Application File Reference**. This information is
    mandatory.

22. To validate the information entered, click on **Validate**.

23. To save the information, click on the **Save Project** button.

## Prior Application Information

Entering information about prior applications is optional since such
information is available to the examiner elsewhere in the application
file wrapper. Any number of prior applications may be included on the
Prior Application Information Screen (Figure 4-15). They will be
displayed in the table in the order entered and may be selected for
editing or deleting.

![](media/image17.png){width="6.052083333333333in"
height="4.614583333333333in"}[]{#_Ref137364286 .anchor}

Figure 4‑15: Prior Application Information Screen

**To enter information about a prior application:**

1.  Enter the **Prior Application Number**. If a prior application
    number is entered then the prior application date becomes mandatory.

```{=html}
<!-- -->
```
24. Enter the **Prior Application Filing Date**. The date format is
    numeric: YYYY-MM-DD.

25. To clear the information in the **Edit Prior Application** area,
    click on **Clear**.

26. To insert the information to the list, select the item you want the
    information to follow, enter the **Prior Application Number** and
    the **Prior Application Filing Date**, and then click on the
    **Insert** button.

27. To replace an entry from the list, select the item, enter the
    **Prior Application Numbe**r and the **Prior Application Filing
    Date**, then click **Replace**.

28. To delete an entry from the list, select the item from the list, and
    then click on the **Delete** button.

29. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

30. To save the information, click on the **Save Project** button.

31. To validate and close, click on the **OK** button.

**Note**: When **OK** is clicked, the data in the edit field(s) will be
inserted into the list when they are different from the selected row.

## Applicant Data

The Application Data Screen (Figure 4-16) allows the user to input
information for an Individual or Organizational applicant. Select
Applicant Data from the Application Steps menu, then select either
Individual or Organization from the next menu. If Individual is
selected, the Individual Applicants Screen (Figure 4-17) will appear. If
Organization is selected, the Organization Applicants Screen (Figure
4-18) will appear.

![](media/image18.png){width="6.497222222222222in"
height="4.959027777777778in"}[]{#_Ref137440674 .anchor}

Figure 4‑16: Application Data Screen

### Individual Applicants

The Individual Applicants Screen (Figure 4-17) allows the user to enter
information about an individual applicant. Only the name(s) of the
applicant(s) will appear on the sequence listing, the spaces for the
other information are for the user's convenience.

**Note**[:]{.smallcaps} The field names in red and marked with asterisks
(Last Name and First Name) are mandatory information.

![](media/image19.png){width="6.0625in" height="5.208333333333333in"}

[]{#__RefHeading___Toc178405786 .anchor}Figure 4‑17: Individual
Applicants Screen

**To enter information about an individual applicant:**

1.  From the Application Steps menu, Select Applicant Data, then Select
    Individual.

```{=html}
<!-- -->
```
32. Enter the User's Last Name (surname).

33. Enter any Suffix the user has on his/her name (e.g., Jr., III).

34. Enter the User's First Name.

35. Enter the User's Middle Initial.

36. Enter the User's Street Address, City, State/Province, Country,
    Zip/Postal Code, Phone Number, Fax Number, and Electronic Mail
    Address.

37. To clear the information about the Individual Applicant, click on
    **Clear**.

38. To insert the information to the list, select the item you want the
    information to follow, enter the **Edit Individual Applicant**
    information, and then click on the **Insert** button.

39. To replace an entry from the list, select the item, enter the **Edit
    Individual Applicant** information, and then click **Replace**.

40. To delete an entry from the list, select the item from the list, and
    then click on the **Delete** button.

41. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

42. To validate and close, click on the **OK** button.

43. To add another applicant to the list, repeat Steps 2-12.

    **Note**[:]{.smallcaps} The phone number, fax number, and zip code
    are no longer validated. Also when OK is clicked, the data in the
    edit field(s) will be inserted into the list when they are different
    from the selected row.

### Organization Applicants 

The Organization Applicants Screen (Figure 4-18) allows the user to
enter information about an organization applicant. As with individual
applicants, only the name of the organization appears on the sequence
listing and the spaces for the other information are for the user's
convenience.

**Note**[:]{.smallcaps} The field name in red and marked with asterisk
(Organization) is mandatory information.

![](media/image20.png){width="5.325694444444444in"
height="4.197916666666667in"}

[]{#__RefHeading___Toc178405787 .anchor}Figure 4‑18: Organization
Applicants Screen

**To enter information about an Organization Applicant:**

1.  From the **Applicant** **Steps** menu, Select Applicant **Data**,
    then Select Organization.

```{=html}
<!-- -->
```
44. Enter the **Organization**'s Name.

45. Enter the Organization's Street Address, City, State/Province,
    Country, Zip/Postal Code, Phone Number, Fax Number, and Electronic
    Mail Address.

46. To clear the information about the Edit Organization Applicant
    portion of the screen, click on **Clear**.

47. To insert the information in the list, select the item you want the
    information to follow, enter the **Edit Organization Applicant**
    information, and then click on the **Insert** button.

48. To replace an entry from the list, select the item, enter the **Edit
    Organization Applicant** information, and then click **Replace**.

49. To delete an entry from the list, select the item from the list, and
    then click on the **Delete** button.

50. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

51. Repeat steps 2 through 8 until all applicant information has been
    included.

52. To validate and close, click on the **OK** button.

    **Note**[:]{.smallcaps} The phone number, fax number, and zip code
    are no longer validated. Also when OK is clicked, the data in the
    edit field(s) will be inserted into the list when they are different
    from the selected row.

# Sequence Data

## Sequence

The Sequence Screen (Figure 5-1) is where you create and modify
sequences. You can create and edit custom codons and custom organism
names from this screen. It also provides a search function where a
genetic sequence may be entered and searched for in the files for this
project. The user will access this screen immediately after PatentIn is
started.

![](media/image21.png){width="6.497222222222222in"
height="4.959027777777778in"}

[]{#__RefHeading___Toc178405788 .anchor}Figure 5‑19: Sequence Screen

**Note**: To begin entering a new sequence you must first have a
sequence name. See Section 5.2.

**To select a sequence for editing:**

1.  Select a sequence name from the list of sequences.

**The following sequence characteristics are displayed:**

-   **Cursor Position -** Shows the current cursor position. This field
    is blank when there is no sequence.

-   **String Length -** Shows the length of the sequence string on the
    line.

-   **Line Number-** Indicates the line number of the cursor position
    relative to the beginning of the string.

### Selecting a Standard Organism

Figure 5-20 enables the user to select an organism name from common
organisms. Included in its capabilities is an attempt to match on
partially input names.

![](media/image22.png){width="6.083333333333333in"
height="4.833333333333333in"}

[]{#__RefHeading___Toc178405789 .anchor}Figure 5‑20: Selecting an
Organism Screen

**To select an organism name:**

1.  Click on the **Standard** button (Sequence Screen).

```{=html}
<!-- -->
```
53. Begin entering characters for the organism you are looking for.

54. Click on the **Apply to all Sequences in the Project** checkbox to
    enable/disable assigning this organism name to all sequences
    currently in the project.

55. Click on the **OK** button to enter the selected organism name.

**Note**[:]{.smallcaps} The Organism in red and marked with asterisks is
mandatory information.

### Creating Default Explanations for \"n"s and \"Xaa"s

PatentIn 3.5 can create default explanations for the entries \"n\" and
\"Xaa\" in the sequence listing that have no user-supplied explanations.
The default explanations take the form of misc_features containing the
location of the variable characters, and the message, \"n is a, c, g, or
t\" for nucleic acid sequence or \"Xaa can be any naturally occurring
amino acid\" for protein sequences. The **Check for missing features**
box on the Sequence Screen can be used to turn this feature on or off.
Users may wish to check the box and press Validate to see if there are
any variable characters not defined by a misc_feature. If the box is
unchecked, PatentIn 3.5 will create any missing misc_features. Users may
create selected definitions by hand and PatentIn 3.5 will provide the
remaining ones.

### Searching for a Sequence

**To search for a specific sequence:**

1.  Enter a particular substring (a feature, for example) in the
    **Search** **bases/proteins** edit field (Figure 5-19).

```{=html}
<!-- -->
```
56. Click on the **Go** button. The cursor will move to the first
    instance of that sub-sequence beginning with its current position.

**Note**[:]{.smallcaps} Each [s]{.smallcaps}earch is limited or
truncated to 60 characters.

### Clearing the Screen

1.  To clear all of the screen about a specific selected sequence, click
    on the **Clear** button, as shown in Figure 5-19.

## Adding a Sequence

The **Add** button on the Sequence Screen provides a means to enter a
sequence name and to select a sequence type from a list of radio buttons
(Figure 5-21).

![](media/image23.png){width="2.6770833333333335in"
height="3.613888888888889in"}

[]{#__RefHeading___Toc178405790 .anchor}Figure 5‑21: Add a Sequence
Screen

**To add a sequence:**

1.  From the Sequence Screen, select the **Add** button. Figure 5-21 is
    displayed.

```{=html}
<!-- -->
```
57. Enter the sequence name into the dialog box.

58. Select the sequence type by clicking on the radio button next to the
    appropriate sequence type.

59. Click **OK**.

You can now enter sequence strings in the edit field at the bottom of
the screen. If you are using Windows XP or Windows Vista, the upper
limit is over 12 million sequence characters.

You can work around these limitations by using import files, rather than
the Sequence Editor, to create and edit sequences.

## Importing a Sequence

The **Import** button on the Sequence Screen provides a means to import
sequences from a file, a project or a PatentIn generated ST.25 sequence
Listing file by selecting one of the radio buttons in Figure 5-22.

![](media/image24.png){width="6.493055555555555in"
height="3.0256944444444445in"}

[]{#__RefHeading___Toc178405791 .anchor}Figure 5‑22: Import Sequence(s)
Screen

1.  To import sequences from a non ST.25 text file, click on the
    **Import** button on the Sequence Screen, and then click on the
    **From File** radio button (See section 5.3.1).

```{=html}
<!-- -->
```
60. To import sequences from another project, click on the **Import**
    button on the Sequence Screen, and then click on the **From
    Project** radio button (See section 5.3.3).

61. To import sequences from PatentIn generated ST.25 sequence listing
    file, click on the **Import** button on the Sequence Screen, and
    then click on the **From PatentIn Generated ST.25 Sequence Listing
    File** radio button (See section 5.3.4).

62. A **Browse** button is provided for each radio button to assist the
    user in providing the file folder and file name and formatting the
    input for multiple file selections. Folder and file names with
    imbedded spaces are accepted.

63. The **Character Filter On** checkbox can be used in conjunction with
    the first radio button: "**From File**:". The default state for this
    box is checked, turning on the function. Deselecting this box will
    allow only files that contain no extraneous errors to be imported.
    Leaving the box checked will still give the user a list of
    characters found to be in error, but the valid characters will be
    imported and placed in the project. Because PatentIn 3.5 allows
    multiple sequences in a single file and thus uses the "\<"
    characters for its header, this character will be understood to be a
    valid character, which will most likely cause a "missing header"
    error message and thus cannot be removed as an extraneous character
    when importing sequences from a non ST.25 text file. For best
    results it is recommended that, the non ST.25 sequence files contain
    only the sequence with spaces and numbering, and that any title or
    other text is deleted prior to importing. For example, if the title
    of the sequence is Genomic Deoxyribonucleic Acid (DNA), PatentIn 3.5
    would filter out the characters \"e,\" \"o\" and \"i\" and so the
    first seven characters of your sequence would be "gnmcdna."

**Note**: For the Protein/3 selection, the data must be imported from a
text file that contains only amino acid abbreviated names as shown in
Appendix C: Conversion Table Between Nucleotide Triplets (Codons) And
One- And Three-Letter Amino Acid Codes, PRT/3 Column. The PRT/3 strings
are converted to PRT/1 characters for subsequent use in the Sequence
Editor. A Protein/3 file without a header can also be imported.

### Format for Multi-Sequence Data Files (Non-ST.25 Sequence Listing File) to be Imported by PatentIn 3.5

A sequence file is an ASCII text file containing one or more sequences.
Each multi-sequence data file must begin with a header having the
following format described in section 5.3.1.1. The header must be the
first non-blank text on its line.

#### Sequence Header

The entire header must be on a single line (Table 5-1).

\<*SequenceName;SequenceType;OrganismName*\>

[]{#__RefHeading___Toc178405829 .anchor}Table 5‑2: Header for Sequence

+-------------------+--------------------------------------------------+
| **Sequence Name** | **The Name of the Sequence**                     |
+-------------------+--------------------------------------------------+
| *SequenceType*    | One of the following:                            |
|                   |                                                  |
|                   | -   DNA                                          |
|                   |                                                  |
|                   | -   RNA                                          |
|                   |                                                  |
|                   | -   DNA/RNA                                      |
|                   |                                                  |
|                   | -   Protein/1                                    |
|                   |                                                  |
|                   | -   PRT                                          |
|                   |                                                  |
|                   | -   PRT/1                                        |
|                   |                                                  |
|                   | -   PRT1                                         |
|                   |                                                  |
|                   | -   Protein/3                                    |
|                   |                                                  |
|                   | -   PRT/3                                        |
|                   |                                                  |
|                   | -   PRT3                                         |
+-------------------+--------------------------------------------------+
| *OrganismName*    | The name of the organism is optional. If it is   |
|                   | omitted, the header looks like:                  |
|                   | \<*SequenceName;SequenceType*;\>                 |
+-------------------+--------------------------------------------------+

**Note**: Notice that there are semi-colon separators. They are always
required.

#### Sequence Data

The sequence data begin on the line following the header. The sequence
data are a string of letters appropriate to the sequence type. The
sequence data may span multiple lines. Sequence data may not contain
spaces. A space signifies the end of the sequence data.

The sequence data are terminated by one or more spaces, or by the start
of the next header. There may be one or more empty lines between the end
of a sequence and the start of the next.

A two-sequence file might look like this Sample ASCII Sequence Data in
Figure 5-23.

\< First Sequence;DNA;Abies alba\>

ttttcttattgtttctcctactgcttatcataatgattgtcgtagtggcttcctcatcgt

ctcccccaccgcctaccacaacgactgccgcagcggattactaatagtatcaccaacagc

ataacaaaaagaatgacgaagagggttgctgatggtgtcgccgacggcgtagcagaagga

gtggcggagggg

\< Second Sequence;RNA; \>

uuuucuuauuguuucuccuacugcuuaucauaaugauugucguaguggcuuccucaucgu

cucccccaccgccuaccacaacgacugccgcagcggauuacuaauaguaucaccaacagc

auaacaaaaagaaugacgaagaggguugcugauggugucgccgacggcguagcagaagga

guggcggagggg

[]{#__RefHeading___Toc178405792 .anchor}Figure 5‑23: Sample ASCII
Sequence Data

### Format for Single Sequence Data Files to be Imported by PatentIn 3.5

A sequence file is an ASCII text file containing one or more sequences.
A single sequence data file does not require a Sequence Header. If the
header is missing, the user is queried for the sequence type in Figure
5-24 and the file is assumed a single sequence data file.

![](media/image25.png){width="2.9680555555555554in"
height="2.2083333333333335in"}

[]{#__RefHeading___Toc178405793 .anchor}Figure 5‑24: Sequence Type
Selection Screen

While the import feature is running, a screen displays the total number
of sequences that have thus far been analyzed. Figure 5-25 shows that a
multi-sequence file named SEQ10000.txt has analyzed 696 sequences at the
time this screen was captured.

![](media/image26.png){width="2.9680555555555554in" height="1.9375in"}

[]{#__RefHeading___Toc178405794 .anchor}Figure 5‑25: Sequences Being
Imported Screen

A Validation Errors screen is displayed if validation errors occur. In
the next example (Figure 5-26), "e" is an invalid character for Sequence
1 of type DNA and Sequence 2 contains an invalid sequence type.

![](media/image27.png){width="5.354166666666667in"
height="4.543055555555555in"}

[]{#__RefHeading___Toc178405795 .anchor}Figure 5‑26: Validation Errors
Screen

### Importing Sequences from a Project

PatentIn provides a mechanism to import sequences from a PatentIn 3.5
project (Figure 5-22).

1.  To use a sequence from a project file, click on the **Import**
    button on the sequence screen (Figure 5-19) then click on the **From
    Project** radio button.

```{=html}
<!-- -->
```
64. The **Browse** button is provided to assist the user in providing
    the file folder and file name.

65. When a project has been selected, a list of sequences in the project
    is displayed.

66. Click on the sequence(s) to be imported.

**Note**[:]{.smallcaps} By holding the Ctrl key down multiple sequences
may be selected.

67. Or select the **Select All** button to select all of the sequences
    (Figure 5-27).

![](media/image28.png){width="4.248611111111111in"
height="3.9569444444444444in"}

[]{#__RefHeading___Toc178405796 .anchor}Figure 5‑27: Select Sequences
From Project Screen

### Importing Sequences from a PatentIn Generated ST.25 Sequence Listing File

PatentIn provides a mechanism to import sequence information from a
PatentIn generated ST.25 sequence listing file. A PatentIn generated
ST.25 sequence listing file is a sequence listing file generated by
PatentIn and is complied with ST.25. The name of the file is composed of
the PatentIn project name followed by "\_ST25.txt". An example of such a
file would be "PatentInProject_ST25.txt".

1.  To import a PatentIn generated ST.25 sequence listing file, press
    the **Import** button on the sequence screen (Figure 5-19) and then
    select the **From PatentIn Generated ST.25 Sequence Listing File**
    radio button on the Import Sequence(s) screen (Figure 5-4).

2.  Select a PatentIn generated ST.25 sequence listing file that has
    "\_ST25.txt" at the end of the file name. The **Browse** button is
    provided to assist the user in selecting the file folder and file
    name.

3.  Click on the **Import** button. PatentIn will acknowledge the user
    with a message box (Figure 5-28) with "The sequence listing will be
    imported to a new PatentIn project" message.

![](media/image29.png){width="3.9583333333333335in" height="1.3125in"}

[]{#__RefHeading___Toc178405797 .anchor}Figure 5‑28: Import to New
Project Message Dialog Screen

4.  Press the **OK** button to close the message box. If the user has
    already a PatentIn project open and the project has not been saved,
    PatentIn will display a dialog box (Figure 5-29) and ask whether to
    save changes to the currently working project. Press the **Yes**
    button to save the changes or the **No** button to discard the
    changes. To cancel the import process, select the **Cancel** button.

![](media/image30.png){width="2.7708333333333335in" height="1.3125in"}

[]{#__RefHeading___Toc178405798 .anchor}Figure 5‑29: Save Project Screen

5.  Once the import process starts, the **Parsing the Applicant Names**
    screen (Figure 5-30) will be displayed.

![](media/image31.png){width="6.497916666666667in"
height="5.111111111111111in"}

[]{#__RefHeading___Toc178405799 .anchor}Figure 5‑30: Parsing Applicant
Names Screen

For each applicant name listed in the ST.25 sequence listing file,
PatentIn displays it in the non-editable **Applicant Name from the
Imported File** box on the **Parsing the Applicant Names** screen. The
user should first identify the type of this applicant name by selecting
the **Individual Applicant Name** or **Organization Applicant Name**
radio button (Organization Applicant Name radio button is selected by
default). The applicant names can be modified in the **Organization
Applicant Name** box or in the individual applicant name text boxes
composed by the **Last Name**, **First Name**, **Middle Initial** and
**Suffix** boxes. Once the type of the applicant name is selected and/or
the applicant name is modified, press the **Add** button to move the
current applicant name to the **Applicant Name List** box as well as to
get and display the next applicant name from the imported file to the
**Applicant Name from the Imported File** box. Repeat this process until
all names are added to the **Applicant Name List** box. Then PatentIn
will acknowledge the user with a message "All applicant names have been
added". Press the **OK** button to close the message box (Figure 5-31).

![](media/image32.png){width="2.6791666666666667in" height="1.3125in"}

[]{#__RefHeading___Toc178405800 .anchor}Figure 5‑31: Added All Names
Message Dialog Screen

To modify any applicant name again after all names have been added to
the **Applicant Name List** box, select the name from the Applicant Name
List box and modify the names in the applicant name text boxes. Press
the **Update** button to save the change. If no more modifications are
needed, press the **Finish** button to close the **Parsing the Applicant
Names** screen. The import process continues.

**Note**: It is necessary for PatentIn users to verify if the imported
sequence information is interpreted and stored in the PatentIn system as
anticipated after the import process since the data may or may not be
converted to be 100% compliant with the imported ST.25 sequence listing.

**Additional Information on Importing PatentIn Generated ST.25 Sequence
Listing:**

-   **Individual Applicant Name Parsing**: While parsing an individual
    applicant name, PatentIn will identify everything before the
    leftmost comma of an applicant name as the last name. When no comma
    is present in the individual applicant name, PatentIn will identify
    the last word of an imported line of applicant name as the last
    name.

-   **Primary Sequences and Supplemental sequences**: Only primary
    sequences will be imported to PatentIn system. All supplemental
    sequences (coding sequence) immediately following the primary
    sequence will not be imported because they will be generated during
    the sequence listing generation. However, all supplemental sequences
    immediately following a suppressed supplemental sequence (a
    supplemental sequences containing less than four amino acids and is
    not present in the imported file) will be imported to PatentIn as
    new protein sequences.

-   **Skipped Sequences**: All skipped sequences will be imported to
    PatentIn. Because a skipped sequence does not have a sequence type,
    PatentIn will ask the user to select a type by displaying the
    **Skipped Sequence Type Selection** screen (Figure 5-32). Press the
    **OK** button after the selection is made.

![](media/image33.png){width="2.7083333333333335in"
height="3.3333333333333335in"}

[]{#__RefHeading___Toc178405801 .anchor}Figure 5‑32: The Skipped
Sequence Type Selection Screen

-   **Sequences with Invalid Type**: If PatentIn encountered a sequence
    with an invalid sequence type while importing, it will display the
    **Invalid Sequence Type Encountered** screen (Figure 5-33) with
    information of the sequence ID, the invalid type and the first 60
    characters of the sequence. Press the **OK** button after the
    correct type is selected.

![](media/image34.png){width="5.645833333333333in"
height="3.638888888888889in"}

[]{#__RefHeading___Toc178405802 .anchor}Figure 5‑33: Invalid Sequence
Type Encountered Screen

-   **A List of Sequences to Be Imported**: After all sequences have
    been parsed, PatentIn displays a list of sequences ready to be
    brought in to PatentIn on the **Select Sequences to Import** screen
    (Figure 5-34). Select the sequence(s) to be imported
    (**Note**[:]{.smallcaps} By holding the Ctrl key down multiple
    sequences may be selected) or press the **Select All** button to
    select all of the sequences (Figure 5-34). Press the **OK** button
    to bring the selected sequences to the PatentIn system.

![](media/image35.png){width="5.5625in" height="5.1875in"}

[]{#__RefHeading___Toc178405803 .anchor}Figure 5‑34: Select Sequences to
Import Screen

-   **Log File**: The parsing messages generated (if there is any)
    during the import process will be recorded in a log file with the
    name \<PatentInProjectName\>\_ ParseFileErrorLog.txt.

## Copying a Sequence

PatentIn uses standard Windows-type edit features.

**To copy a sequence:**

1.  Highlight the sequence to be copied.

```{=html}
<!-- -->
```
68. Click on the **Edit** menu, then click **Copy** (Figure 5-35).

![](media/image36.png){width="6.497222222222222in"
height="4.959027777777778in"}

[]{#__RefHeading___Toc178405804 .anchor}Figure 5‑35: Edit Menu

## Pasting a Sequence

**To paste a sequence:**

1.  Position the cursor where the copied material is to be inserted.

```{=html}
<!-- -->
```
69. Click on the **Edit**, and then click **Paste**.

## Deleting a Sequence

**To delete a sequence:**

1.  Position the cursor where the copied material is to be deleted.

2.  Click on the **Delete** button.

## Skip a Sequence

When a sequence is skipped, PatentIn 3.5 will not generate anything
between the \<210\> and the \<400\> for this sequence.

**To skip a sequence:**

1.  Select the sequence to be skipped.

```{=html}
<!-- -->
```
70. Click on the **Skip this sequence** checkbox to turn on the skip
    sequence flag on the Sequence Screen (Figure 5-19). PatentIn 3.5
    will automatically generate the sequence number and \"000\" for the
    \<400\> in the sequence listing.

## Restoring a Sequence

When a sequence has been deleted, it can be restored until the current
project update is terminated.

**To restore a sequence:**

1.  Click on the **Restore** button on the main screen. The Sequence
    Recovery Screen (Figure 5-36) appears.

```{=html}
<!-- -->
```
71. Select the sequence(s) to be restored.

72. Click on the **Restore** button.

![](media/image37.png){width="3.1458333333333335in"
height="3.9868055555555557in"}

[]{#__RefHeading___Toc178405805 .anchor}Figure 5‑36: Sequence Recovery
Screen

## Reordering Sequences

The Recorder Sequence Screen (Figure 5-37) provides the user with the
means to compare the current sequence order and the new sequence order.
The Current Sequence Order is displayed on the left of the screen. It
displays the sequences in the order that the sequences were entered into
the application. The New Sequence Order, displayed on the right,
displays the sequences in the order that the user specifies by selecting
a contiguous group of sequences from the left side and selecting a
single sequence on the right side that they are to be placed after.

![](media/image38.png){width="6.429166666666666in" height="5.2625in"}

[]{#__RefHeading___Toc178405806 .anchor}Figure 5‑37: Reorder Sequences
Screen

**To reorder sequences:**

1.  Select the sequence row(s) to move from the sequence List A.

```{=html}
<!-- -->
```
73. From the sequence List B select a sequence after which the
    sequence(s) chosen from the List A should follow. Press the Reorder
    button for the new sequence order.

74. Repeat steps 1-2 until the sequences are in the desired order.

## Changing a Sequence Type

The **AlterSeqType** button on the Sequence Screen provides a means to
change the type of a non-protein sequence to one of the sequence types
listed on the Change Sequence Type Screen, as shown in Figure 5-38.

![](media/image39.png){width="2.8125in" height="3.4270833333333335in"}

[]{#__RefHeading___Toc178405807 .anchor}Figure 5‑38: Change Sequence
Type Screen

**To change the type of an existing non-protein sequence:**

1.  From the Sequence Screen, select the sequence to be converted.

```{=html}
<!-- -->
```
75. Click on the **AlterSeqType** button. The Change Sequence Type
    screen appears.

76. Select a different sequence type by clicking on the radio button
    next to the appropriate sequence type.

77. Click **Convert** button.

After the sequence type conversion, the custom codons defined in the
custom codon table will be automatically converted to reflect the
targeted sequence type. The resulting duplicates of custom codons (if
they exist) will be deleted from the custom codon table.

## Validating Sequences

**To validate the sequences:**

1.  On the Sequence Screen, click on the **Validate** button. A message
    screen will inform you if there was an error, otherwise "Validation
    is successful" will appear on the status bar.

**Note**: For the Sequence Data, validation is done for the selected
sequence name.

## Saving Sequences

**To save a sequence:**

1.  On the Sequence Screen (Figure 5-19), click on the **Save Project**
    button. Your work will be saved in its current state.

**Note**: It is important to remember while working with very large or
complex projects that saving often can prevent hours of rework,
especially when there is a system failure.

## Reloading a Saved Project

The **Reload Saved Project** button is supplied, at the request of some
of the users, to quickly load the current project from its last saved
state (Figure 5-19).

## Adding Custom Codons

The Custom Codons Input Screen (Figure 5-39) provides the means to add
Custom Codons to the list of standard codons on the user workstation.
This screen is accessed from the Application Steps menu Figure 4-13 by
selecting the Define Custom Codons item.

![](media/image40.png){width="5.199305555555555in"
height="4.115277777777778in"}

[]{#__RefHeading___Toc178405808 .anchor}Figure 5‑39: Custom Codons Input
Screen

**To add a custom codon:**

1.  Select the Define Custom Codons item from the Application Steps menu
    in Figure 4-1.

```{=html}
<!-- -->
```
78. Select an **Amino Acid** from the drop-down list (Figure 5-40).

79. Enter the **Custom Codon**.

80. Click on the **Insert** button.

**Note**[:]{.smallcaps} The format of this screen has changed. It now
allows the user to see all of the custom codons on a single screen
instead of having to select each amino acid individually.

**To delete a custom codon:**

1.  Click on the Custom Codon in the list.

```{=html}
<!-- -->
```
81. Click on the **Delete** button.

![](media/image41.png){width="5.645833333333333in" height="4.46875in"}

[]{#__RefHeading___Toc178405809 .anchor}Figure 5‑40: Amino Acid Drop
Down List Screen

## Adding a Custom Organism

The Custom Organism Input Screen (Figure 5-41) provides the means to add
a custom organism to the list of custom organisms. It also enables you
to select a custom organism to enter on the Sequence Screen (Figure
5-19). This screen is accessed from the Sequence Screen by selecting the
**Custom** button. The user enters the custom organism into the screen,
and then can manipulate the list by adding or deleting organisms.

![](media/image42.png){width="4.625in" height="4.6875in"}

[]{#__RefHeading___Toc178405810 .anchor}Figure 5‑41: Custom Organism
Input Screen

**To add a custom organism:**

1.  Select the **Custom** button from the Sequence Screen.

```{=html}
<!-- -->
```
82. Enter the Custom Organism.

83. Click on the **Insert** button.

**To delete a custom organism:**

1.  Click on the Custom Organism in the list.

```{=html}
<!-- -->
```
84. Click on the **Delete** button.

**To replace a custom organism:**

1.  Click on the Custom Organism in the list.

```{=html}
<!-- -->
```
85. Enter the Custom Organism.

86. Click on the **Replace** button.

**To enter a custom organism on the Sequence Screen:**

1.  Select the Organism so that the name appears in the "Please enter a
    custom organism name:" box.

```{=html}
<!-- -->
```
87. Click on the **OK** button.

**To apply a custom organism to all of the sequences in the project:**

1.  Click the check box marked: Apply to all Sequences in the Project.

```{=html}
<!-- -->
```
88. Click on the **OK** button.

## Artificial Sequence or Unknown Organism

An Artificial Sequence or Unknown organism must have a comment about the
organism. After either Artificial Sequence or Unknown is entered into
the Organism Name field and the user has moved to another field, an
automatic pop-up box will appear as shown in Figure 5-42.

![](media/image43.png){width="4.655555555555556in"
height="2.2604166666666665in"}

[]{#__RefHeading___Toc178405811 .anchor}Figure 5‑42: Artificial
Sequence/Unknown Organism Comment

1.  Select the **Standard** button from the Sequence Screen.

```{=html}
<!-- -->
```
89. Select either Unknown or Artificial from the list of standard
    organisms.

90. Tab or move to another cell, the comment box, Figure 5-42, will
    automatically pop-up when a definition of the organism is required.

91. Enter an appropriate comment for the organism. This information will
    be placed in a \<223\> field when the sequence listing is generated.

92. Check the **Apply to All Unknown/Artificial Organisms** box if the
    comment is to be applied to all of the Artificial Sequence Organisms
    and/or Unknown Organisms that have no current comment. The ways to
    use this function is to input all the sequences, label the
    appropriate ones artificial and/or unknown, then apply the comment
    to one of the sequences with the box checked. The same comment will
    then appear for all the artificial sequences in the project.

**Note**[:]{.smallcaps} This field can also be accessed by choosing
Application Steps\|Artificial Sequence/Unknown Comment (Figure 4-1).

**Note**[:]{.smallcaps} The content of this box should be as descriptive
as possible while remaining as terse as possible.

**Note**[:]{.smallcaps} The \<223\> section of the sequence listing is
updated by using either an Artificial Sequence/Unknown Organism or a
misc_feature. The \<223\> section is the comment or other information,
respectively. PatentIn 3.5 generates "Synthetic Construct" for the
\<223\> section in the protein sequence generated from any coding region
in a nucleotide sequence where Artificial or Unknown is used as the
organism.

# Feature Data

## Sequence Features 

The Feature Screen (Figure 6-43) enables you to create and modify
features pertaining to a sequence. You can access this screen by
selecting **Feature Data** from the Application Steps Menu (Figure
4-13), or by selecting the **Fea** button on the PatentIn toolbar. The
features that are displayed apply to the sequence that is currently
selected on the Sequence Screen.

![](media/image44.png){width="6.28125in" height="5.229166666666667in"}

[]{#__RefHeading___Toc178405812 .anchor}Figure 6‑43: Features Screen

**To enter information about a Feature:**

1.  Check the **Join All Code Sequence (CDS)** box if the sequence
    contains more than one CDS and the CDSs are to be joined.

```{=html}
<!-- -->
```
93. Click on the **Names** button to access the list of Nucleotide Names
    for **Feature Name/Key**.

94. Enter the **"Relevant Residue From"** and **"To"** sequence position
    numbers.

95. Click in the **Other Information** box to provide other information.
    This is where you would document X in a protein sequence or n in a
    base sequence. The Feature Name/Key should be misc_feature.

96. To clear the **Edit Feature** portion of the screen, click on the
    **Clear** button.

97. To insert an entry from the **Feature List**, click on the
    **Insert** button.

98. To replace an entry from the **Feature List**, highlight it and
    click on the **Replace** button.

99. To delete an entry from the **Feature List**, highlight it and click
    on the **Delete** button.

100. To validate the information entered, click on **Validate**. Data
     entered in the table (Insert) is then validated. Information in the
     edit area, that has not yet been inserted, is not validated.

101. To save the information, click on the **Save Project** button.

102. To validate and close, click on the **OK** button.

103. To cancel the information, click on the **Cancel** button.

104. To access the help information, click on the **Help** button.

**Note**[:]{.smallcaps} The **Join All CDSs** disappears and appears
based on whether there is more than one CDS in the Feature List.

**Note**[:]{.smallcaps} The \<223\> section of the sequence listing is
updated by using either an Artificial Sequence/Unknown Organism or a
misc_feature. The \<223\> section is the comment or other information,
respectively. Also there is an automatic expansion of the possible
resolutions for "Xaa."

### Feature Key Selection

The Feature Names/Key Selection Screen (Figure 6-44) allows the user to
select a Nucleotide name.

![](media/image45.png){width="5.614583333333333in" height="4.53125in"}

[]{#__RefHeading___Toc178405813 .anchor}Figure 6‑44: Feature Names/Key
Selection Screen

**To select a nucleotide name:**

1.  Select the **Names** button on the Feature Screen (Figure 6-43).

```{=html}
<!-- -->
```
2.  Begin typing on the **Nucleotide** field.

```{=html}
<!-- -->
```
105. Or, select a feature name from the list by clicking on the feature
     name or using up/down arrow keys.

106. Click on **OK** to accept the selection and return to the Feature
     Screen (Figure 6-43).

### Additional Information Required for Modified_Base

The Feature Names/Key Selection Screen () automatically reveals an
additional window when modified_base is selected.

![](media/image46.wmf){width="5.291666666666667in"
height="4.946527777777778in"}[]{#_Ref501932744 .anchor}

Figure 6‑45: Feature Names/Key Selection Screen with Modified Base

**To add information about the modified_base:**

1.  Select the pull-down arrow on the box marked "Add the following
    modified_base to the Other Information."

2.  Select modified_base from the list (Figure 6-45).

3.  Click on **OK** (Figure 6-45).

### Additional Information on CDS (Coding Sequence)

When a CDS is specified for a polynucleotide sequence, the DNA sequence
will appear in "mixed" format with the DNA split up into codons and the
appropriate amino acid beneath each codon. This is exactly what
specification of the "exon" feature will do. Selection of CDS, however,
forces PatentIn 3.5 to automatically generate the polypeptide sequence
as a "supplemental" sequence.

### Further Definition of "N" or "Xaa"

If the variable character "n" appears in a polynucleotide sequence or
the variable "Xaa" appears in a polypeptide sequence, ST.25 requires
further definition. This is to be provided in the Other Information
field using misc_feature. PatentIn will copy the definition of "n" into
the supplemental polypeptide sequence and translate it to "Xaa."

### Selecting an Amino Acid

The Feature Name/Key Selection Screen (Figure 6-46) automatically
reveals an additional window when LIPID is selected.

![](media/image47.png){width="5.614583333333333in" height="4.53125in"}

[]{#__RefHeading___Toc178405815 .anchor}Figure 6‑46: Feature Names/Key
Selection Screen with LIPID Selected

**To select an amino acid name:**

1.  Select the **Names** button on the Feature Screen (Figure 6-43).

```{=html}
<!-- -->
```
2.  Begin typing on the **Amino Acid** field.

3.  Click on the down arrow to open the drop down list (Figure 6‑5),
    select a name from the list.

```{=html}
<!-- -->
```
107. Click on **OK** to accept the selection and return to the Feature
     Screen (Figure 6-46).

**To add information about a LIPID:**

1.  Select the pull down arrow on the box marked Add the following LIPID
    to the Other Information field.

```{=html}
<!-- -->
```
108. Select the LIPID information from the list.

109. Click on the **OK** button (Figure 6-46).

### Additional Information for MOD_RES

The Feature Names/Key Selection Screen (Figure 6-47) automatically
reveals an additional two windows when MOD_RES is selected.

![](media/image48.png){width="5.614583333333333in" height="4.53125in"}

[]{#__RefHeading___Toc178405816 .anchor}Figure 6‑47: Feature Names/Key
Selection Screen with MOD_RES Selected

**To select an amino acid name:**

1.  Select the **Names** button on the Feature Screen (Figure 6-43).

```{=html}
<!-- -->
```
2.  Begin typing on the **Amino Acid** field.

```{=html}
<!-- -->
```
3.  Click on the down arrow to open the drop down list (Figure 6‑2),
    select a name from the list.

```{=html}
<!-- -->
```
110. Click on **OK** to accept the selection and return to the Features
     Screen.

     To add information about the MOD_RES:

```{=html}
<!-- -->
```
1.  Select the pull down arrow on the first box in the "Add the
    following MOD_RES to the Other Information field."

```{=html}
<!-- -->
```
111. Select the appropriate information from the list (Figure 6-6).

112. Click on the **OK** button (Figure 6-47).

![](media/image49.png){width="5.614583333333333in" height="4.53125in"}

[]{#__RefHeading___Toc178405817 .anchor}Figure 6‑48: First MOD_RES Pull
Down List

113. Select the pull down arrow on the second box in the "Add the
     following MOD_RES to the Other Information field."

```{=html}
<!-- -->
```
5.  Select the appropriate information from the list (Figure 6-49).

```{=html}
<!-- -->
```
6.  Click on the **OK** button (Figure 6-47).

![](media/image50.png){width="5.940972222222222in"
height="5.231944444444444in"}

[]{#__RefHeading___Toc178405818 .anchor}Figure 6‑49: Second MOD_RES Pull
Down List

# Publication Data

## Publication Type Screen 

The Publication Type Screen (Figure 7-50) provides access to four
screens for entering publication information. They are Journal,
Database, Patent, and Thesis. You can access this screen by selecting
Publication Data from the Application Steps menu.

![](media/image51.png){width="6.497222222222222in"
height="4.959027777777778in"}

[]{#__RefHeading___Toc178405819 .anchor}Figure 7‑50: Publication Type
Screen

**To select a publications type:**

1.  From the pull down menu, **Application Steps,** click on
    **Publication Data.**

## Journals Publication Information

The Journals Publications Information Screen (Figure 7-51) provides the
user with a means to input published supporting scientific literature
with the patent application.

[]{#_Ref476978663 .anchor}![](media/image52.png){width="6.09375in"
height="5.552083333333333in"}

Figure 7‑51: Journals Publication Information Screen

**To enter information about a journal publication:**

1.  From the Application Steps menu, select **Publication Data**, select
    **Journal**.

```{=html}
<!-- -->
```
2.  Enter the **Database Name/Accession Number**.

3.  Enter the **Database Entry Date**.

4.  Enter the name of the **Author(s)**.

5.  Enter the **Publication Title**.

6.  Select the **Journal** name from the drop-down pick list. If the
    name is not on the list, you may enter it.

7.  Enter the **Volume**.

8.  Enter the **Issue**.

9.  Enter the **Publication Date**.

10. Enter the **Page Ranges**.

11. Enter the **Relevant Residues From** and **To** sequence position
    numbers.

12. Click on the Clear button to clear the **Journal Publications**
    portion of the screen.

13. To insert an entry from the **Journal List**, click on the
    **Insert** button.

14. To replace an entry from the **Journal List**, highlight it, change
    the entry in the top of the screen, and click on the **Replace**
    button.

15. To delete an entry from the **Journal List**, highlight it and click
    on the **Delete** button.

16. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    **Journal Publications** edit area, that has not yet been inserted,
    is not validated.

17. To save the information, click on the **Save Project** button.

18. To validate and close, click on the **OK** button.

19. To proceed to other **Publication** **Data**, click on the **To
    Databases, To Patents or To Theses** button.

## Databases Publication Information

The Databases Publication Information Screen (Figure 7-52) provides the
user with a means to input published supporting scientific database with
the patent application.

![](media/image53.png){width="5.1375in" height="4.209722222222222in"}

[]{#__RefHeading___Toc178405821 .anchor}Figure 7‑52: Databases
Publication Information Screen

To enter information about a database publication:

1.  From the Application Steps select Publications Data, then select
    Database.

```{=html}
<!-- -->
```
2.  Enter the **Database Name/Accession Number**.

3.  Enter the **Database Entry Date**.

4.  Enter the **Relevant Residues From** and **To** sequence position
    numbers.

5.  Click on the **Clear** button to clear the **Databases** part of the
    screen.

6.  To insert an entry into the **Database List**, click on the
    **Insert** button.

7.  To replace an entry from the **Database List**, highlight it, change
    the entry in the top of the screen, and click on the **Replace**
    button.

8.  To delete an entry from the **Database List**, highlight it and
    click on the **Delete** button.

9.  To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

10. To save the information, click on the **Save Project** button.

11. To validate and close, click on the **OK** button.

12. To proceed to other Publication Data, click on the **To Journals**,
    **To Patents,** or **To Theses** button.

## Patents Publications Information 

The Patents Publication Information Screen (Figure 7-53) provides the
user with a means to input published supporting patent publication
information with the patent application.

![](media/image54.png){width="4.581944444444445in"
height="3.926388888888889in"}

[]{#__RefHeading___Toc178405822 .anchor}Figure 7‑53: Patents Publication
Information Screen

**To enter information about a patent publication:**

1.  From the Application Steps select Publications Data, and then select
    Patent.

```{=html}
<!-- -->
```
2.  Enter the **Database Name/Accession Number**.

3.  Enter the **Database Entry Date**.

4.  Enter the **Document Number**.

5.  Enter the **Filing Date**.

6.  Enter the **Publication Date**.

7.  Enter the **Title**.

8.  Enter the **Relevant Residues From** and **To** sequence position
    numbers.

9.  Click on the Clear button to clear the **Patents** portion of the
    screen.

10. To insert an entry into the **Patent List**, click on the **Insert**
    button.

11. To replace an entry from the **Patent List**, highlight it, change
    the entry in the top of the screen, and click on the **Replace**
    button.

12. To delete an entry from the **Patent List**, highlight it and click
    on the **Delete** button.

13. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

14. To save the information, click on the **Save Project** button.

15. To validate and close, click on the **OK** button.

16. To proceed to other **Publication Data**, click on the **To
    Databases, To Journals** or **To Theses** button.

## Theses Publication Information

The Theses Publication Information Screen (Figure 7-54) provides the
user with a means to input published supporting thesis publication
information with the patent application.

![](media/image55.png){width="4.2625in" height="3.667361111111111in"}

[]{#__RefHeading___Toc178405823 .anchor}Figure 7‑54: Theses Publications
Information Screen

**To enter information about a thesis publication:**

1.  From the Application Steps select Publications Data, and then select
    [T]{.underline}hesis.

```{=html}
<!-- -->
```
2.  Enter the **Database Name/Accession Number**.

3.  Enter the **Database Entry Date**.

4.  Enter the name of the **Author(s)**.

5.  Enter the **Title**.

6.  Enter the **Publication Date**.

7.  Enter the **Page Ranges**.

8.  Enter the **Relevant Residues From** and **To** sequence position
    numbers.

9.  Click on the **Clear** button to clear the **Theses** portion of the
    screen.

10. To insert an entry into the **Thesis List**, click on the **Insert**
    button.

11. To replace an entry from the **Thesis List**, highlight it, change
    the entry in the top of the screen, and click on the **Replace**
    button.

12. To delete an entry from the **Thesis List**, highlight it and click
    on the **Delete** button.

13. To validate the information entered, click on **Validate**. Data
    entered in the table (Insert) is then validated. Information in the
    edit area, that has not yet been inserted, is not validated.

14. To save the information, click on the **Save Project** button.

15. To validate and close, click on the **OK** button.

16. To proceed to other **Publication Data**, click on the **To
    Databases**, **To Journals**, or **To Patents** button.

# Creating a Sequence Listing Project File

## Sequence Listing File

The sequence listing file includes all the information required by
ST.25. PatentIn 3.5 will generate a sequence listing in text format. The
name of the sequence listing is consisted of the current PatentIn
project name appended with "\_ST25.txt." This ST25 file is placed in the
directory containing the project.

## Generating a Sequence Listing File

The Sequence Generation Screen (Figure 8-55) notifies the user that the
Generate process is about to occur and gives the option to be notified
as errors occur during the process.

![](media/image56.png){width="6.502083333333333in"
height="2.1444444444444444in"}

[]{#__RefHeading___Toc178405824 .anchor}Figure 8‑55: Sequence Generation
Screen

**To generate a sequence listing:**

1.  Select **Generate** **Sequence Listing** from the **Application
    Steps** menu in Figure 4-13 or by selecting the **Gen** button on
    the PatentIn toolbar.

```{=html}
<!-- -->
```
2.  Click in the box next to the "Pause after each error" if you wish to
    be notified of an error in the sequence data when it occurs.

3.  Click in the box next to "View listing or error log when done" if
    you wish to see the listing or error log immediately after the
    generation. The listing/log will be automatically displayed when the
    generation has terminated.

4.  Click on the **Start** the sequence generation.

5.  Click on the **Continue** button to continue validation, Figure 8-2.

6.  Click on the **Cancel** button to cancel validation.

7.  If an error message is displayed and "Pause after each error
    message" was selected, an error message will appear and validation
    will pause.

![](media/image57.png){width="6.502083333333333in"
height="2.1444444444444444in"}

[]{#__RefHeading___Toc178405825 .anchor}Figure 8‑56: Second Sequence
Generation Screen

## Viewing a Sequence Listing File

**To view a sequence listing project file:**

1.  If sequence generation succeeded and **View** **listing or error log
    when done** was selected, the generated sequence listing will be
    shown automatically on the View Results Window (Figure 8-57). If
    **View** **listing or error log when done** was not selected, you
    can view the same results by selecting **View/Print Sequence
    Listing** or **View/Print Error Report** from the **Project** menu.

![](media/image58.png){width="6.486111111111111in"
height="3.6034722222222224in"}

[]{#__RefHeading___Toc178405826 .anchor}Figure 8‑57: View Results Window

**Special Note for users with very large sequences and large numbers of
sequences**[:]{.smallcaps} The USPTO has located a viewer that works
well for very large text files. A 60-day evaluation version is
downloadable at [http://www.fileviewer.com](http://www.fileviewer.com/).
The viewer is named "V" and the version is 7.2 (SR-2). USPTO
successfully viewed 60 MB and 120 MB files using an earlier version of
the V software and that it was on a laptop with Windows 98 (LocalAdmin
may be required for installation). The USPTO is not recommending this
product but is naming it as an example of the type of product available
for this use.

## Copying the Sequence Listing to a Disk

The Copy to Disk Screen (Figure 8-58) provides the user with the means
to name the drive name to where the file is to be copied, the filename
for the copied file and the type of copied file.

![](media/image59.png){width="5.84375in" height="4.34375in"}

[]{#__RefHeading___Toc178405827 .anchor}Figure 8‑58: Copy to Disk Screen

**To copy a sequence listing:**

1.  Select **[C]{.underline}opy to Disk** from the
    **[A]{.underline}pplication Steps** menu in Figure 4-13.

```{=html}
<!-- -->
```
114. Select a drive name (Figure 8-58) in the Save in field.

115. Select the type .txt or .zip in the Save as type field.

116. Enter a file name in the File name field.

117. Click on the Save to submit the application.

If **.txt** is selected, PatentIn checks to see if there is enough free
disk space to receive the listing file. If so, the file will be copied
to the selected location. If not, PatentIn will suggest **.zip**.

**Note**: The .zip file works only with floppy disk(s), hard drive, and
network drive.

**Note**: In general, if a hard drive is selected, the user will be
prompted to select a removable medium as the target for this copy.

**Note**: The save to a Compact Disk (CD) expects the CD to function
like any other drive. That is, the user can perform explorer type
commands as if the CD were a disk drive (example: F drive). If your CD
does not have such a driver, the file can still be located on your hard
drive where it was generated. It is the project name with "\_ST25.txt"
appended to it.

# List of Acronyms

Table 9-3 lists the specific acronyms that are used within this
document.

[]{#__RefHeading___Toc178405830 .anchor}Table 9‑3: Acronyms

  ------------------ ----------------------------------------------------
  **Acronyms**       **Definitions**

  AN                 Applicant Name

  ASCII              American Standard Code for Information Interchange

  CDS                Coding Sequence

  DID                Data Item Description

  DLL                Dynamic Link Library

  DNA                Deoxyribonucleic Acid

  DOS                Disc Operating System

  EPO                European Patent Office

  ET                 Equatorial

  FQT                Functional Qualification Test

  LTR                Long Terminal Repeat

  MB                 Megabytes

  MS                 Microsoft

  PC                 Personal Computer

  RBS                Ribosome Binding Site

  STS                Sequence Tagged Site

  UM                 User\'s Manual

  US                 United States

  USPTO              United States Patent and Trademark Office

  WIPO               World Intellectual Property Organization

  WPI                Web PatentIn

  XP                 Microsoft Experience
  ------------------ ----------------------------------------------------

####### Field Identifiers, Lengths and Types

Table A-1 includes a complete list of all field names that appear in the
data entry screens and their corresponding field identifiers, field
lengths, and field types. Field identifiers are used to separate
PatentIn data into raw data files and sequence listing project files.

[]{#__RefHeading___Toc178405831 .anchor}Table A‑: Field Name,
Identifier, Size, and Type

+-----------+----------------------+--------------+--------------------+
| **Field   | **Field Name**       | **Field      | **Field Type**     |
| Ide       |                      | Length**     |                    |
| ntifier** |                      |              | **A-alpha N-       |
|           |                      |              | Numeric**          |
+===========+======================+==============+====================+
| N/A       | Project Name         | 8            | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<110\>   | Applicant Name       | 1200         | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<120\>   | Title of Invention   | 240          | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<130\>   | File Reference       | 60           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<140\>   | Current Application  | 23           | AN                 |
|           | Number               |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<141\>   | Current Filing Date  | 8            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<150\>   | Earlier Application  | 23           | AN                 |
|           | Number               |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<151\>   | Earlier Filing Date  | 8            | N                  |
+-----------+----------------------+--------------+--------------------+
| N/A       | Sequence File Name   | 8            | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<160\>   | Number of Sequences  | 5            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<170\>   | Software             | 60           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<210\>   | Information for SEQ  | 5            | N                  |
|           | ID No.               |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<211\>   | Length               | 6            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<212\>   | Type                 | 3            | A                  |
+-----------+----------------------+--------------+--------------------+
| \<213\>   | Organism             | 60           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<220\>   | Feature              | 0            | B                  |
+-----------+----------------------+--------------+--------------------+
| \<221\>   | Name/key             | 20           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<222\>   | Location             | 12           | N                  |
+-----------+----------------------+--------------+--------------------+
| \<223\>   | Other Information    | 260          | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<300\>   | Publication          | 0            | B                  |
|           | Information          |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<301\>   | Authors              | 120          | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<302\>   | Title (of            | 120          | AN                 |
|           | Publication)         |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<303\>   | Journal (name)       | 40           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<304\>   | Volume               | 5            | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<305\>   | Issue                | 5            | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<306\>   | Pages                | 20           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<307\>   | Date                 | 30           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<308\>   | Database Accession   | 45           | AN                 |
|           | Number               |              |                    |
+-----------+----------------------+--------------+--------------------+
| \<309\>   | Database Entry Date  | 8            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<310\>   | Document Number      | 18           | AN                 |
+-----------+----------------------+--------------+--------------------+
| \<311\>   | Filing Date          | 8            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<312\>   | Publication Date     | 8            | N                  |
+-----------+----------------------+--------------+--------------------+
| \<313\>   | Relevant Residues    | 20           | N                  |
+-----------+----------------------+--------------+--------------------+
| \<400\>   | Sequence Description | 100,000      | AN                 |
+-----------+----------------------+--------------+--------------------+

####### Country Codes

Table B- includes a complete list of country codes that are used when
completing the Current Application Number field in the Project Data
Screen (Figure 4-14) and the **Prior Application Number** field in the
**Prior Application Information Screen** (Figure 4-3).

[]{#__RefHeading___Toc178405832 .anchor}Table B‑: Country Codes

  -----------------------------------------------------------------------
  **Code**       **Country**
  -------------- --------------------------------------------------------
  AF             Afghanistan

  OA             African Intellectual Property Organization (OAPI)

  AP             African Regional Industrial Property Organization
                 (ARIPO)

  AL             Albania

  DZ             Algeria

  AO             Angola

  AI             Anguilla

  AG             Antigua & Barbuda

  AR             Argentina

  AU             Australia

  AT             Austria

  BS             Bahamas

  BH             Bahrain

  BD             Bangladesh

  BB             Barbados

  BE             Belgium

  BZ             Belize

  BX             Benelux Trademark Office and Benelux Designs Office

  BJ             Benin

  BM             Bermuda

  BT             Bhutan

  BO             Bolivia

  BW             Botswana

  BR             Brazil

  VG             British Virgin Islands

  BN             Brunei Darussalam

  BG             Bulgaria

  BF             Burkina Faso

  BU             Burma

  BI             Burundi

  CM             Cameroon

  CA             Canada

  CV             Cape Verde

  KY             Cayman Islands

  CF             Central African Republic

  TD             Chad

  CL             Chile

  CN             China

  CO             Columbia

  KM             Comoros

  CG             Congo

  CR             Costa Rica

  CI             Cote d\'Ivoire

  CU             Cuba

  CY             Cyprus

  CS             Czechoslovakia

  KH             Democratic Kampuchea

  KP             Democratic People\'s Republic of Korea

  YD             Democratic Yemen

  DK             Denmark

  DJ             Djibouti

  DM             Dominica

  DO             Dominican Republic

  EC             Ecuador

  EG             Egypt

  SV             El Salvador

  GQ             Equatorial Guinea

  ET             Ethiopia

  EP             European Patent Office (EPO)

  FK             Falkland Islands (Malvinas)

  FJ             Fiji

  FI             Finland

  FR             France

  GA             Gabon

  GM             Gambia

  DD             German Democratic Republic

  DE             Germany, Federal Republic of

  GH             Ghana

  GI             Gibraltar

  GR             Greece

  GD             Grenada

  GT             Guatemala

  GN             Guinea

  GW             Guinea-Bissau

  GY             Guyana

  HT             Haiti

  VA             Holy See

  HN             Honduras

  HK             Hong Kong

  HU             Hungary

  IS             Iceland

  IN             India

  ID             Indonesia

  IR             Iran (Islamic Republic of)

  IQ             Iraq

  IE             Ireland

  IL             Israel

  IT             Italy

  JM             Jamaica

  JP             Japan

  JO             Jordan

  KE             Kenya

  KI             Kiribati

  KW             Kuwait

  LA             Laos

  LB             Lebanon

  LS             Lesotho

  LR             Liberia

  LY             Libya

  LI             Liechtenstein

  LU             Luxembourg

  MG             Madagascar

  MW             Malawi

  MY             Malaysia

  MV             Maldives

  ML             Mali

  MT             Malta

  MR             Mauritania

  MU             Mauritius

  MX             Mexico

  MC             Monaco

  MN             Mongolia

  MS             Montserrat

  MA             Morocco

  MZ             Mozambique

  NR             Nauru

  NP             Nepal

  NL             Netherlands

  AN             Netherlands Antilles

  NZ             New Zealand

  NI             Nicaragua

  NE             Niger

  NG             Nigeria

  NO             Norway

  OM             Oman

  PK             Pakistan

  PA             Panama

  PG             Papua New Guinea

  PY             Paraguay

  PE             Peru

  PH             Philippines

  PL             Poland

  PT             Portugal

  QA             Qatar

  KR             Republic of Korea

  RO             Romania

  RW             Rwanda

  KN             Saint Christopher & Nevis

  SH             Saint Helena

  LC             Saint Lucia

  VC             Saint Vincent & the Grenadines

  WS             Samoa

  SM             San Marino

  ST             Sao Tome & Principe

  SA             Saudi Arabia

  SN             Senegal

  SC             Seychelles

  SL             Sierra Leone

  SG             Singapore

  SB             Solomon Islands

  SO             Somalia

  ZA             South Africa

  SU             Soviet Union

  ES             Spain

  LK             Sri Lanka

  SD             Sudan

  SR             Suriname

  SZ             Swaziland

  SE             Sweden

  CH             Switzerland

  SY             Syria

  TW             Taiwan, Province of China

  TH             Thailand

  TG             Togo

  TO             Tonga

  TT             Trinidad & Tobago

  TN             Tunisia

  TR             Turkey

  TV             Tuvalu

  UG             Uganda

  AE             United Arab Emirates

  GB             United Kingdom

  TZ             United Republic of Tanzania

  US             United States of America

  UY             Uruguay

  VU             Vanuatu

  VE             Venezuela

  VN             Viet Nam

  WO             World Intellectual Property Organization (WIPO)

  YE             Yemen

  YU             Yugoslavia

  ZR             Zaire

  ZM             Zambia

  ZW             Zimbabwe
  -----------------------------------------------------------------------

####### Conversion Table Between Nucleotide Triplets (Codons) and One- and Three Letter Amino Acid Codes

Table C- provides a list of acceptable characters to be used for hand
keying PRT/1 data into the sequence description field, importing PRT/3
data, and converting PRT/1 data in the sequence description field. The
nucleotide triplet equivalent data is utilized during sequence listing
project file generation when all CDS-featured codons (nucleotide
triplets) are translated into an amino abbreviated name (PRT/3).

[]{#__RefHeading___Toc178405833 .anchor}Table C‑: Exchange Nucleotide
Characters and Amino Characters

  ---------------------------------------------------------------------------
  **PRT/1**   **PRT/3**   **Nucleotide Equivalent**
  ----------- ----------- ---------------------------------------------------
  A           Ala         gcu, gcc, gca, gcg, gct

  R           Arg         cgu, cgc, cga, cgg, cgt, aga, agg

  N           Asn         aau, aac, aat

  D           Asp         gau, gac, gat

  B           Asx         

  C           Cys         ugu, ugc, tgt, tgc

  Q           Gln         caa, cag

  E           Glu         gaa, gag

  Z           Glx         

  G           Gly         ggu, ggc, gga, ggg, ggt

  H           His         cau, cac, cat

  I           Ile         auu, auc, aua, att, atc, ata

  L           Leu         uua, uug, cuu, cuc, cua, cug, tta, ttg, ctt, ctc,
                          cta, ctg

  K           Lys         aaa, aag

  M           Met         aug, atg

  F           Phe         uuu, uuc, ttt, ttc

  P           Pro         ccu, ccc, cca, ccg, cct

  S           Ser         ucu, ucc, uca, ucg, tct, tcc, tca, tcg, agu, agc,
                          agt

  T           Thr         acu, acc, aca, acg, act

  W           Trp         ugg, tgg

  Y           Tyr         uau, uac, tat, tac

  V           Val         guu, guc, gua, gug, gtt, gtc, gta, gtg

  X           Xaa         any set containing "n"
  ---------------------------------------------------------------------------

####### Nucleotide Sequence Features

Table D- provides a list (in alphanumeric order) of **Nucleotide**
sequence features that are displayed in the Features Screen when you
have previously selected DNA or RNA as the **Sequence Type** and clicked
on the **Names** button. A list of nucleotides appears in a pick list
after clicking on the down arrow at the end of the **Nucleotide** box.
After clicking on a sequence feature in the pick list, the sequence
feature name appears in the **Feature** **Name/Key** field (\<221\>).

[]{#__RefHeading___Toc178405834 .anchor}Table D‑: Nucleotide Sequence
Features

+--------------+-------------------------------------------------------+
| **Key**      | **Description**                                       |
+==============+=======================================================+
| allele       | a related individual or strain contains stable,       |
|              | alternative forms of the same gene which differs from |
|              | the presented sequence at this location (and perhaps  |
|              | others)                                               |
+--------------+-------------------------------------------------------+
| attenuator   | \(1\) region of DNA at which regulation of            |
|              | termination of transcription occurs, which controls   |
|              | the expression of some bacterial operons;             |
|              |                                                       |
|              | \(2\) sequence segment located between the promoter   |
|              | and the first structural gene that causes partial     |
|              | termination of transcription                          |
+--------------+-------------------------------------------------------+
| C_region     | constant region of immunoglobulin light and heavy     |
|              | chains, and T-cell receptor alpha, beta, and gamma    |
|              | chains; includes one or more exons depending on the   |
|              | particular chain                                      |
+--------------+-------------------------------------------------------+
| CAAT_signal  | CAAT box; part of a conserved sequence located about  |
|              | 75 bp up-stream of the start point of eukaryotic      |
|              | transcription units which may be involved in RNA      |
|              | polymerase binding; consensus=gg (c or t) caatct      |
+--------------+-------------------------------------------------------+
| CDS          | coding sequence; sequence of nucleotides that         |
|              | corresponds with the sequence of amino acids in a     |
|              | protein (location includes stop codon); feature       |
|              | includes amino acid conceptual translation            |
+--------------+-------------------------------------------------------+
| conflict     | independent determinations of the \"same\" sequence   |
|              | differ at this site or region                         |
+--------------+-------------------------------------------------------+
| D-loop       | displacement loop; a region within mitochondrial DNA  |
|              | in which a short stretch of RNA is paired with one    |
|              | strand of DNA, displacing the original partner DNA    |
|              | strand in this region; also used to describe the      |
|              | displacement of a region of one strand of duplex DNA  |
|              | by a single stranded invader in the reaction          |
|              | catalyzed by RecA protein                             |
+--------------+-------------------------------------------------------+
| D-segment    | diversity segment of immunoglobulin heavy chain, and  |
|              | T-cell receptor beta chain                            |
+--------------+-------------------------------------------------------+
| enhancer     | a cis-acting sequence that increases the utilization  |
|              | of (some) eukaryotic promoters, and can function in   |
|              | either orientation and in any location (upstream or   |
|              | downstream) relative to the promoter                  |
+--------------+-------------------------------------------------------+
| exon         | region of genome that codes for portion of spliced    |
|              | mRNA; may contain 5\'UTR, all CDSs, and 3\'UTR        |
+--------------+-------------------------------------------------------+
| GC_signal    | GC box; a conserved GC-rich region located upstream   |
|              | of the start point of eukaryotic transcription units  |
|              | which may occur in multiple copies or in either       |
|              | orientation; consensus=gggcgg                         |
+--------------+-------------------------------------------------------+
| gene         | region of biological interest identified as a gene    |
|              | and for which a name has been assigned                |
+--------------+-------------------------------------------------------+
| iDNA         | intervening DNA; DNA which is eliminated through any  |
|              | of several kinds of recombination                     |
+--------------+-------------------------------------------------------+
| intron       | a segment of DNA that is transcribed, but removed     |
|              | from within the transcript by splicing together the   |
|              | sequences (exons) on either side of it                |
+--------------+-------------------------------------------------------+
| J_segment    | joining segment of immunoglobulin light and heavy     |
|              | chains, and T-cell receptor alpha, beta, and gamma    |
|              | chains                                                |
+--------------+-------------------------------------------------------+
| LTR          | long terminal repeat, a sequence directly repeated at |
|              | both ends of a defined sequence, of the sort          |
|              | typically found in retroviruses                       |
+--------------+-------------------------------------------------------+
| mat_peptide  | mature peptide or protein coding sequence; coding     |
|              | sequence for the mature or final peptide or protein   |
|              | product following post-translational modification;    |
|              | the location does not include the stop codon (unlike  |
|              | the corresponding CDS)                                |
+--------------+-------------------------------------------------------+
| misc_binding | site in nucleic acid which covalently or              |
|              | non-covalently binds another moiety that cannot be    |
|              | described by any other Binding key (primer_bind or    |
|              | protein_bind)                                         |
+--------------+-------------------------------------------------------+
| mis          | feature sequence is different from that presented in  |
| c_difference | the entry and cannot be described by any other        |
|              | Difference key (conflict, unsure, old_sequence,       |
|              | mutation, variation, allele, or modified_base)        |
+--------------+-------------------------------------------------------+
| misc_feature | region of biological interest which cannot be         |
|              | described by any other feature key; a new or rare     |
|              | feature                                               |
+--------------+-------------------------------------------------------+
| misc_recomb  | site of any generalized, site-specific or replicative |
|              | recombination event where there is a breakage and     |
|              | reunion of duplex DNA that cannot be described by     |
|              | other recombination keys (iDNA and virion) or         |
|              | qualifiers of source key (/insertion_seq,             |
|              | /transposon, /proviral)                               |
+--------------+-------------------------------------------------------+
| misc_RNA     | any transcript or RNA product that cannot be defined  |
|              | by other RNA keys (prim_transcript, precursor_RNA,    |
|              | mRNA, 5\'clip, 3\'clip, 5\'UTR, 3\'UTR, exon, CDS,    |
|              | sig_peptide, transit_peptide, mat_peptide, intron,    |
|              | polyA_site, rRNA, tRNA, scRNA, and snRNA)             |
+--------------+-------------------------------------------------------+
| misc_signal  | any region containing a signal controlling or         |
|              | altering gene function or expression that cannot be   |
|              | described by other Signal keys (promoter,             |
|              | CAAT_signal, TATA_signal, -35_signal, -10_signal,     |
|              | GC_signal, RBS, polyA_signal, enhancer, attenuator,   |
|              | terminator, and rep_origin)                           |
+--------------+-------------------------------------------------------+
| mi           | any secondary or tertiary structure or conformation   |
| sc_structure | that cannot be described by other Structure keys      |
|              | (stem_loop and D-loop)                                |
+--------------+-------------------------------------------------------+
| m            | the indicated nucleotide is a modified nucleotide and |
| odified_base | should be substituted for by the indicated molecule   |
|              | (given in the mod_base qualifier value)               |
+--------------+-------------------------------------------------------+
| mRNA         | messenger RNA; includes 5\' untranslated region       |
|              | (5\'UTR), coding sequences (CDS, exon) and 3\'        |
|              | untranslated region (3\'UTR)                          |
+--------------+-------------------------------------------------------+
| mutation     | a related strain has an abrupt, inheritable change in |
|              | the sequence at this location                         |
+--------------+-------------------------------------------------------+
| N_region     | extra nucleotides inserted between rearranged         |
|              | immunoglobulin segments                               |
+--------------+-------------------------------------------------------+
| old_sequence | the presented sequence revises a previous version of  |
|              | the sequence at this location                         |
+--------------+-------------------------------------------------------+
| polyA_signal | recognition region necessary for endonuclease         |
|              | cleavage of an RNA transcript that is followed by     |
|              | polyadenylation; consensus=aataaa                     |
+--------------+-------------------------------------------------------+
| polyA_site   | site on an RNA transcript to which will be added      |
|              | adenine residues by post-transcriptional              |
|              | polyadenylation                                       |
+--------------+-------------------------------------------------------+
| p            | any RNA species that is not yet the mature RNA        |
| recursor_RNA | product; may include 5\' clipped region (5\'clip),    |
|              | 5\' untranslated region (5\'UTR), coding sequences    |
|              | (CDS, exon), intervening sequences (intron), 3\'      |
|              | untranslated region (3\'UTR), and 3\' clipped region  |
|              | (3\'clip)                                             |
+--------------+-------------------------------------------------------+
| pri          | primary (initial, unprocessed) transcript; includes   |
| m_transcript | 5\' clipped region (5\'clip), 5\' untranslated region |
|              | (5\'UTR), coding sequences (CDS, exon), intervening   |
|              | sequences (intron), 3\' untranslated region (3\'UTR), |
|              | and 3\' clipped region (3\'clip)                      |
+--------------+-------------------------------------------------------+
| primer_bind  | non-covalent primer binding site for initiation of    |
|              | replication, transcription, or reverse transcription; |
|              | includes site(s) for synthetic, for example, PCR      |
|              | primer elements                                       |
+--------------+-------------------------------------------------------+
| promoter     | region on a DNA molecule involved in RNA polymerase   |
|              | binding to initiate transcription                     |
+--------------+-------------------------------------------------------+
| protein_bind | non-covalent protein binding site on nucleic acid     |
+--------------+-------------------------------------------------------+
| RBS          | ribosome binding site                                 |
+--------------+-------------------------------------------------------+
| r            | region of genome containing repeating units           |
| epeat_region |                                                       |
+--------------+-------------------------------------------------------+
| repeat_unit  | single repeat element                                 |
+--------------+-------------------------------------------------------+
| rep_origin   | origin of replication; starting site for duplication  |
|              | of nucleic acid to give two identical copies          |
+--------------+-------------------------------------------------------+
| rRNA         | mature ribosomal RNA; the RNA component of the        |
|              | ribonucleoprotein particle (ribosome) which assembles |
|              | amino acids into proteins                             |
+--------------+-------------------------------------------------------+
| S_region     | switch region of immunoglobulin heavy chains;         |
|              | involved in the rearrangement of heavy chain DNA      |
|              | leading to the expression of a different              |
|              | immunoglobulin class from the same B-cell             |
+--------------+-------------------------------------------------------+
| satellite    | many tandem repeats (identical or related) of a short |
|              | basic repeating unit; many have a base composition or |
|              | other property different from the genome average that |
|              | allows them to be separated from the bulk (main band) |
|              | genomic DNA                                           |
+--------------+-------------------------------------------------------+
| scRNA        | small cytoplasmic RNA; any one of several small       |
|              | cytoplasmic RNA molecules present in the cytoplasm    |
|              | and (sometimes) nucleus of a eukaryote                |
+--------------+-------------------------------------------------------+
| sig_peptide  | signal peptide coding sequence; coding sequence for   |
|              | an N-terminal domain of a secreted protein; this      |
|              | domain is involved in attaching nascent polypeptide   |
|              | to the membrane; leader sequence                      |
+--------------+-------------------------------------------------------+
| snRNA        | small nuclear RNA; any one of many small RNA species  |
|              | confined to the nucleus; several of the snRNAs are    |
|              | involved in splicing or other RNA processing          |
|              | reactions                                             |
+--------------+-------------------------------------------------------+
| source       | identifies the biological source of the specified     |
|              | span of the sequence; this key is mandatory; every    |
|              | entry will have, as a minimum, a single source key    |
|              | spanning the entire sequence; more than one source    |
|              | key per sequence is permissible                       |
+--------------+-------------------------------------------------------+
| stem_loop    | hairpin; a double-helical region formed by            |
|              | base-pairing between adjacent (inverted)              |
|              | complementary sequences in a single strand of RNA or  |
|              | DNA                                                   |
+--------------+-------------------------------------------------------+
| STS          | Sequence Tagged Site; short, single-copy DNA sequence |
|              | that characterizes a mapping landmark on the genome   |
|              | and can be detected by PCR; a region of the genome    |
|              | can be mapped by determining the order of a series of |
|              | STSs                                                  |
+--------------+-------------------------------------------------------+
| TATA_signal  | TATA box; Goldberg-Hogness box; a conserved AT-rich   |
|              | septamer found about 25 bp before the start point of  |
|              | each eukaryotic RNA polymerase II transcript unit     |
|              | which may be involved in positioning the enzyme for   |
|              | correct initiation; consensus=tata(a or t)a(a or t)   |
+--------------+-------------------------------------------------------+
| terminator   | sequence of DNA located either at the end of the      |
|              | transcript or adjacent to a promoter region that      |
|              | causes RNA polymerase to terminate transcription; may |
|              | also be site of binding of repressor protein          |
+--------------+-------------------------------------------------------+
| tra          | transit peptide coding sequence; coding sequence for  |
| nsit_peptide | an N-terminal domain of a nuclear-encoded organellar  |
|              | protein; this domain is involved in                   |
|              | post-translational import of the protein into the     |
|              | organelle                                             |
+--------------+-------------------------------------------------------+
| tRNA         | mature transfer RNA, a small RNA molecule (75-85      |
|              | bases long) that mediates the translation of a        |
|              | nucleic acid sequence into an amino acid sequence     |
+--------------+-------------------------------------------------------+
| unsure       | author is unsure of exact sequence in this region     |
+--------------+-------------------------------------------------------+
| V_region     | variable region of immunoglobulin light and heavy     |
|              | chains, and T-cell receptor alpha, beta, and gamma    |
|              | chains; codes for the variable amino terminal         |
|              | portion; can be made up from V_segments, D_segments,  |
|              | N_regions, and J_segments                             |
+--------------+-------------------------------------------------------+
| V_segment    | variable segment of immunoglobulin light and heavy    |
|              | chains, and T-cell receptor alpha, beta, and gamma    |
|              | chains; codes for most of the variable region         |
|              | (V_region) and the last few amino acids of the leader |
|              | peptide                                               |
+--------------+-------------------------------------------------------+
| variation    | a related strain contains stable mutations from the   |
|              | same gene (for example, RFLPs, polymorphisms, etc.)   |
|              | which differ from the presented sequence at this      |
|              | location (and possibly others)                        |
+--------------+-------------------------------------------------------+
| 3\'clip      | 3\'-most region of a precursor transcript that is     |
|              | clipped off during processing                         |
+--------------+-------------------------------------------------------+
| 3\'UTR       | region at the 3\' end of a mature transcript          |
|              | (following the stop codon) that is not translated     |
|              | into a protein                                        |
+--------------+-------------------------------------------------------+
| 5\'UTR       | region at the 5\' end of a mature transcript          |
|              | (preceding the initiation codon) that is not          |
|              | translated into a protein                             |
+--------------+-------------------------------------------------------+
| -10_signal   | pribnow box; a conserved region about 10 bp upstream  |
|              | of the start point of bacterial transcription units   |
|              | which may be involved in binding RNA polymerase;      |
|              | consensus=tataat                                      |
+--------------+-------------------------------------------------------+
| -35_signal   | a conserved hexamer about 35 bp upstream of the start |
|              | point of bacterial transcription units;               |
|              | consensus=ttgaca \[ \] or tgttgaca \[ \]              |
+--------------+-------------------------------------------------------+

####### Amino Acid Sequence Features

Table E- provides a list (in alphabetical order) of **AminoAcids**
sequence features that are displayed in the Features Screen when you
have previously selected PRT as the **Sequence Type** and clicked on the
**Names** button. The listed sequence features appear in a pick list
after clicking on the down arrow at the end of the **AminoAcids** box.
After clicking on a sequence feature in the pick list, the sequence
feature name appears in the **Feature** **Name/Key** field.

[]{#__RefHeading___Toc178405835 .anchor}Table E‑: Amino Acid Sequence
Features

  -----------------------------------------------------------------------
  **Key**          **Description**
  ---------------- ------------------------------------------------------
  ACT_SITE         amino acid(s) involved in the activity of an enzyme

  BINDING          binding site for any chemical group (co-enzyme,
                   prosthetic group, etc.); the chemical nature of the
                   group is given in the description field

  CA_BIND          extent of a calcium-binding region

  CARBOHYD         glycosylation site; the nature of the carbohydrate (if
                   known) is given in the description field

  CHAIN            extent of a polypeptide chain in the mature protein

  CONFLICT         different papers report differing sequences

  DISULFID         disulfide bond; the 'FROM' and 'TO' endpoints
                   represent the two residues which are linked by an
                   intra-chain disulfide bond; if the 'FROM' and 'TO'
                   endpoints are identical, the disulfide bond is an
                   interchain one and the description field indicates the
                   nature of the cross-link

  DNA_BIND         extent of a DNA-binding region

  DOMAIN           extent of a domain of interest on the sequence; the
                   nature of that domain is given in the description
                   field

  HELIX            secondary structure: Helices, for example,
                   Alpha-helix, 3(10) helix, or Pi-helix

  INIT_MET         the sequence is known to start with an initiator
                   methionine

  LIPID            covalent binding of a lipidic moiety

  MAT_PEPTIDE      mature peptide; sequence of the mature or final
                   peptide or protein product following
                   post-translational modification

  METAL            binding site for a metal ion; the description field
                   indicates the nature of the metal

  MISC_FEATURE     region of biological interest which cannot be
                   described by any other feature key; a new or rare
                   feature

  MOD_RES          post-translational modification of a residue

  MUTAGEN          site which has been experimentally altered

  NON_CONS         non consecutive residues; indicates that two residues
                   in a sequence are not consecutive and that there are a
                   number of unsequenced residues between them

  NON_TER          the residue at an extremity of the sequence is not the
                   terminal residue; if applied to position 1, this
                   signifies that the first position is not the
                   N-terminus of the complete molecule; if applied to the
                   last position, it signifies that this position is not
                   the C-terminus of the complete molecule; there is no
                   description field for this key

  NP_BIND          extent of a nucleotide phosphate binding region; the
                   nature of the nucleotide phosphate is indicated in the
                   description field

  PEPTIDE          extent of a released active peptide

  PROPEP           extent of a propeptide

  REPEAT           extent of an internal sequence repetition

  SIGNAL           extent of a signal sequence (prepeptide)

  SIMILAR          extent of a similarity with another protein sequence;
                   precise information, relative to that sequence is
                   given in the description field

  SITE             any other interesting site on the sequence

  STRAND           secondary structure: Beta-strand, for example,
                   Hydrogen bonded beta-strand, or Residue in an isolated
                   beta-bridge

  THIOETH          thioether bond; the 'FROM' and 'TO' endpoints
                   represent the two residues which are linked by the
                   thioether bond

  THIOLEST         thiolester bond; the 'FROM' and 'TO' endpoints
                   represent the two residues which are linked by the
                   thiolester bond

  TRANSIT          extent of a transit peptide (mitochondrial,
                   chloroplastic, or for a microbody)

  TRANSMEM         extent of a transmembrane region

  TURN             secondary structure Turns, for example, H-bonded turn
                   (3-turn, 4-turn or 5-turn)

  UNSURE           uncertainties in the sequence; used to describe
                   region(s) of a sequence or which the authors are
                   unsure about the sequence assignment

  VARIANT          authors report that sequence variants exist

  VARSPLIC         description of sequence variants produced by
                   alternative splicing

  ZN_FING          extent of a zinc finger region
  -----------------------------------------------------------------------

####### Data Tables for Mod_Res Sequence Features

Appendix F provides a list (in alphabetical order) of additional
modified residue (MOD_RES) **Sequence Features** that are displayed in
the Features Screen when you have previously selected PRT as the
**Sequence Type**, and MOD_RES from the listed sequence features in the
pick list. After clicking on a sequence feature in the pick list,
**MOD_RES** appears in the **Feature** **Name/Key** field (\<221\>), and
the first **Add the following MOD-RES to the Other Information field**
for MOD_RES (Table F-) and second **Add the following MOD-RES to the
Other Information field** for MOD_RES (Table F-) sequence features
appears. You can select from either one or both of the **Add the
following MOD-RES to the Other Information field**s, and the data will
appear in the **Other Information** field (\<223\>).

[]{#__RefHeading___Toc178405836 .anchor}Table F‑: First Data Table for
MOD_RES Sequence Features

  -----------------------------------------------------------------------
  **Key**                         **Description**
  ------------------------------- ---------------------------------------
  (none)                          blank space (default option)

  ACETYLATION                     N-terminal or other

  AMIDATION                       Generally at the c-terminal of a mature
                                  active peptide

  BLOCKED                         Undetermined n- or c-terminal blocking
                                  group

  FORMYLATION                     Of the n-terminal methionine

  GAMMA-CARBOXYGLUTAMIC ACID      Of asparagine, aspartic acid, proline
  HYDROXYLATION                   or lysine

  METHYLATION                     Generally of lysine or arginine

  PHOSPHORYLATION                 Of serine, threonine, tyrosine,
                                  aspartic acid or histidine

  PYRROLIDONE CARBOXYLIC ACID     N-terminal glutamate which has formed
                                  an internal cyclic lactam

  SULFATATION                     Generally of tyrosine
  -----------------------------------------------------------------------

[]{#__RefHeading___Toc178405837 .anchor}Table F‑: Second Data Table for
MOD_RES Sequences

  -----------------------------------------------------------------------
  **Symbol**              **Meaning**
  ----------------------- -----------------------------------------------
  (none)                  Blank space (default option)

  Aad                     2-Aminoadipic acid

  bAad                    3-Aminoadipic acid

  bAla                    beta-Alanine, beta-Aminopropionic acid

  Abu                     2-Aminobutyric acid

  4Abu                    4-Aminobutyric acid, piperidinic acid

  Acp                     6-Aminocaproic acid

  Ahe                     2-Aminoheptanoic acid

  Aib                     2-Aminoisobutyric acid

  bAib                    3-Aminoisobutyric acid

  Apm                     2-Aminopimelic acid

  Dbu                     2,4 Diaminobutyric acid

  Des                     Desmosine

  Dpm                     2,2'-Diaminopimelic acid

  Dpr                     2,3-Diaminopropionic acid

  EtGly                   N-Ethylglycine

  EtAsn                   N-Ethylasparagine

  Hyl                     Hydroxylysine

  aHyl                    allo-Hydroxylysine

  3Hyp                    3-Hydroxyproline

  4Hyp                    4-Hydroxyproline

  Ide                     Isodesmosine

  aIle                    allo-Isoleucine

  MeGly                   N-Methylglycine, sarcosine

  MeIle                   N-Methylisoleucine

  MeLys                   6-N-Methyllysine

  MeVal                   N-Methylvaline

  Nva                     Norvaline

  Nle                     Norleucine

  Orn                     Ornithine
  -----------------------------------------------------------------------

####### Additional Lipid Sequence Features

Table G- provides a list (in alphabetical order) of additional lipid
sequence features that are displayed in the Features Screen when you
have previously selected PRT as the **Sequence Type**, and **LIPID**
from the listed sequence features in the pick list. After clicking on a
**Sequence Feature** in the **Sequence Feature Pick List**, lipid
appears in the **Feature Name/Key** field (\<221\>) and the **Add the
following LIPID to the Other Information field** appears. When you
select from the **Add the following LIPID to the Other Information
field,** the data appears in the **Other Information** field (\<223\>).

[]{#__RefHeading___Toc178405838 .anchor}Table G‑: Additional Lipid
Sequence Features

  -----------------------------------------------------------------------
  **Key**                **Description**
  ---------------------- ------------------------------------------------
  (none)                 blank space (default option)

  MYRISTATE              Myristate group attached through an amide bond
                         to the N-terminal glycine residue of the mature
                         form of a protein or to an internal lysine
                         residue

  PALMITATE              Palmitate group attached through a thioether
                         bond to a cysteine residue or through an ester
                         bond to a serine or threonine residue

  FARNESYL               Farnesyl group attached through a thioether bond
                         to a cysteine residue

  GERANYL-GERANYL        Geranyl-geranyl group attached through a
                         thioether bond to a cysteine residue

  GPI-ANCHOR             Glycosyl-phosphatidylinositol (GPI) group linked
                         to the alpha-carboxyl group of the C-terminal
                         residue of the mature form of a protein

  N-ACYL DIGLYCERIDE     N-terminal cysteine of the mature form of a
                         prokaryotic lipoprotein with an amide-linked
                         fatty acid and a glyceryl group to which two
                         fatty acids are linked by ester linkages
  -----------------------------------------------------------------------

####### Acceptable Characters In The Sequence Description Field

Table H- provides an acceptable list of characters used as a filter for
hand keying or importing DNA or RNA data into the sequence description
field. PRT/1 and PRT/3 data lists are used during sequence listing
project file generation when all single letter protein data is
translated into amino abbreviated name (PRT/3) data.

[]{#__RefHeading___Toc178405839 .anchor}Table H‑: Acceptable Characters
in the Sequence Description Field

  ------------ -------------- --------------- --------------- ---------------
  **DNA**      **RNA**        **DNA/RNA**     **Protein/1**   **Protein/3**

  a            a              a               A               Ala

  g            g              g               C               Cys

  c            c              c               D               Asp

  t                           t               E               Glu

               u              u               F               Phe

  r            r              r               G               Gly

  y            y              y               H               His

  m            m              m               I               Ile

  k            k              k               K               Lys

  s            s              s               L               Leu

  w            w              w               M               Met

  b            b              b               N               Asn

  d            d              d               P               Pro

  h            h              h               Q               Gln

  v            v              v               R               Arg

  n            n              n               S               Ser

                                              T               Thr

                                              V               Val

                                              W               Trp

                                              Y               Tyr

                                              B               Asx

                                              Z               Glx

                                              X               Xaa
  ------------ -------------- --------------- --------------- ---------------

####### Additional Modified_Base Sequence Features

Table I- provides a list (in alphabetical order) of additional
**modified_base** sequence features that are displayed in the Features
Screen when you have previously selected DNA or RNA as the **Sequence
Type**, and **modified_base** from the listed sequence features in the
pick list. After clicking on a sequence feature in the list,
**modified_base** appears in the **Feature** **Name/Key** field
(\<221\>), and the **Add the following modified_base to the Other
Information** field appears in the Features Screen. The user selects
from the pick lists, and the data appears in the **Other Information**
field (\<223\>).

[]{#__RefHeading___Toc178405840 .anchor}Table I‑: Modified_base Sequence
Features

  -------------------------------------------------------------------------------------
  **Symbol**   **Meaning**
  ------------ ------------------------------------------------------------------------
  ac4c         4-acetylcytidine

  chm5u        5-(carboxyhydroxymethyl)uridine

  cm           2\'-O-methylcytidine

  cmnm5s2u     5-carboxymethylaminomethyl-2-thiouridine

  cmnm5u       5-carboxymethylaminomethyluridine

  d            dihydrouridine

  fm           2\'-O-methylpseudouridine

  gal q        beta, D-galactosylqueuosine

  gm           2\'-O-methylguanosine

  I            inosine

  i6a          N6-isopentenyladenosine

  m1a          1-methyladenosine

  m1f          1-methylpseudouridine

  m1g          1-methylguanosine

  m1I          1-methylinosine

  m22g         2,2-dimethylguanosine

  m2a          2-methyladenosine

  m2g          2-methylguanosine

  m3c          3-methylcytidine

  m5c          5-methylcytidine

  m6a          N6-methyladenosine

  m7g          7-methylguanosine

  mam5u        5-methylaminomethyluridine

  mam5s2u      5-methoxyaminomethyl-2-thiouridine

  man q        beta, D-mannosylqueuosine

  mcm5s2u      5-methoxycarbonylmethyl-2-thiouridine

  mcm5u        5-methoxycarbonylmethyluridine

  mo5u         5-methoxyuridine

  ms2i6a       2-methylthio-N6-isopentenyladenosine

  ms2t6a       N-((9-beta-D-ribofuranosyl-2-methylthiopurine-6-yl)carbamoyl)threonine

  mt6a         N-((9-beta-D-ribofuranosylpurine-6-yl)N-methylcarbamoyl)threonine

  mv           uridine-5-oxyacetic acid-methylester

  o5u          uridine-5-oxyacetic acid

  osyw         wybutoxosine

  p            pseudouridine

  q            queuosine

  s2c          2-thiocytidine

  s2t          5-methyl-2-thiouridine

  s2u          2-thiouridine

  s4u          4-thiouridine

  t            5-methyluridine

  t6a          N-((9-beta-D-ribofuranosylpurine-6-yl)-carbamoyl)threonine

  tm           2\'-O-methyl-5-methyluridine

  um           2\'-O-methyluridine

  yw           wybutosine

  x            3-(3-amino-3-carboxy-propyl) uridine, (acp3) u
  -------------------------------------------------------------------------------------

####### Technical Notes

######## Microsoft® Access Notes

(Section J.1 is only applicable to PatentIn with versions prior to
PatentIn 3.4.)

PatentIn 3.1, PatentIn 3.2 and PatentIn 3.3 were packaged with a
Microsoft® Access 97 program, patin2xconvert.mdb that contains links to
the standard database files that PatentIn 2.1 uses. In order to enable
the user to view the directory, the Link Table Manager must be
installed. Similarly, the Data Access files must include dBase 5 in
order to read the PatentIn 2.1 files.

######### Installing Microsoft® Access 97

These general instructions are for Office 97.

1.  Run Setup from the CD.

```{=html}
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```
17. Select Custom installation. The typical install does not install all
    of the necessary components.

18. Select Microsoft® Access.

19. Click on the Change Options button.

20. Select Advanced Wizards.

21. Return to main screen.

22. Select Data Access.

23. Click on the Change Options button.

24. Select Database Drivers.

25. Click on the Change Options button.

26. Select dBase & Microsoft® FoxPro Drivers.

27. Return to main screen.

28. Finish installation (or Add).

#########  Hints and Tips

1.  Patin2xconvert.mdb must be in the same directory as the CWPI.exe and
    must have the help directory in it.

```{=html}
<!-- -->
```
29. Patin2xconvert.mdb refreshes (updates) its links each time an import
    is done.

30. Patin2xconvert.mdb can be opened independently to verify that all of
    the Microsoft® Access components are available.

    a.  The Link Table Manager is found in the Tools\|Add-Ins in Office
        97 and in Database Utilities in Office 2000.

    b.  The drivers can be verified by selecting File \| Get External
        Data \| Link Tables... The From File Types should include dBase
        5 (\*.dbf).

31. No relationships are maintained in patin2xconvert.mdb.

32. No code/queries are run from patin2xconvert.mdb.

33. Exploring data from patin2xconvert.mdb, though sometimes necessary,
    is not recommended since it is possible to update the linked data
    itself. (Be sure the data is backed-up if this is new to you.)

34. MDAC, a distributable component from Microsoft®, may not be
    sufficient to run this import.

######## General Hints and Tips

1.  The installation requires some Dynamic Link Library (DLL)
    registration for each machine.

```{=html}
<!-- -->
```
35. PatentIn 3.5 uses long-names.

36. In order to reduce the amount of processing of very, very long
    sequences, paste does not pre-scan (validate) the data.

37. The file submission command, Copy to Disk, copies a file already on
    your hard drive to an external medium. In general, it cannot be used
    to copy to your hard drive.

38. Help files are ASCII files than can be locally updated, including
    translated to a native language.

39. Screens that will not appear or only flicker are usually a symptom
    of an installation that was not specifically installed on this
    machine.

40. Windows XP defaults to not showing the underlines on the toolbar
    without pressing the Alt-key.

41. To access PatentIn menu without a mouse, do the following:

    a.  Press the Alt key to activate the menu.

    b.  Release the Alt key.

    c.  Press an access key from the main menu to select a pull-down
        menu.

    d.  Press an access key from the pull-down menu to complete the
        action.

42. To activate a button on PatentIn screen without a mouse, do the
    following:

    a.  Press and hold the Alt key.

    b.  Press the access key of the button.

Although no future enhancement releases are envisioned, maintenance
releases may be necessary; however, unreported problems cannot be fixed.

######## Installation and Testing Notes

#########  PatentIn Installation and Repair

PatentIn can be downloaded onto your computer from the USPTO web page
<http://www.uspto.gov/web/offices/pac/patin/patentinrel.htm>. Before the
installation of PatentIn 3.5, be sure to close all running applications
on your computer and then follow the instructions found on the Web page
to download PatentIn 3.5 and install it on your PC.

A user will be asked to reinstall PatentIn 3.5 while trying to run
PatentIn 3.5. This occurs when PatentIn 3.5 detects the registry keys
required to run PatentIn 3.5 are missing. This may be due to
uninstalling an earlier version of PatentIn. Reinstalling PatentIn 3.5
will rebuild the required registry keys to run PatentIn 3.5 and it will
not cause you to loose any previously saved PatentIn data. If a user
starts the PatentIn 3.5 reinstallation without uninstalling PatentIn 3.5
first, the following screen will be prompted to the user. Select the
"[R]{.underline}epair" radio button as shown in Figure J-, press the
"[N]{.underline}ext" button and follow the installation instructions to
complete the PatentIn repair operation. A user may also choose to
uninstall PatentIn 3.5 first and then reinstall the PatentIn 3.5
software (Figure J-).

![](media/image60.png){width="5.270833333333333in"
height="4.083333333333333in"}

[]{#__RefHeading___Toc137961134 .anchor}Figure J‑: PatentIn Repair and
Uninstall

######### Testing Configurations

During testing the following configurations were used:

-   Microsoft® Windows 95 (Only applicable to PatentIn with versions
    prior to PatentIn 3.4)

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-   Version 4.00.950 B

-   Internet Explorer: 3.0(4.70.1158).

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```
-   Microsoft® Windows 98 (Only applicable to PatentIn with versions
    prior to PatentIn 3.4)

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```
-   Version 4.10.2222 A

-   Internet Explorer 5.00.2614.3500.

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```
-   Microsoft® Windows NT (Only applicable to PatentIn with versions
    prior to PatentIn 3.4)

```{=html}
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```
-   Version 4.00,1381

-   Internet Explorer 6.0.2800.1106.

```{=html}
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```
-   Microsoft® Windows 2000 Professional (Only applicable to PatentIn
    with versions prior to PatentIn 3.4)

```{=html}
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```
-   Version 5.00.2195

-   Internet Explorer 6.0.2800.1106.

```{=html}
<!-- -->
```
-   Microsoft® Windows ME (Only applicable to PatentIn with versions
    prior to PatentIn 3.4)

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```
-   This was not formally tested. However, one of our beta testers has
    informed us that no problems were found with this version.

```{=html}
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```
-   Microsoft® Windows XP Professional

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```
-   Version 2002

-   Internet Explorer 6.0.2800.1106.

```{=html}
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```
-   Microsoft® Windows Vista Ultimate, Microsoft® Windows Vista Home
    Basic and Microsoft® Windows Home Premium

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```
-   Processor : Intel Core 2 CPU 6400 @ 2.13GHz

-   Memory : 1006MB

-   System Type : 32-bit Operating System

-   Internet Explorer 6.0.2800.1106.

Although there is no way to test all configurations inclusively, it is
believed that PatentIn will not negatively impact any of the above.

#########  Internet Explorer Considerations

Internet Explorer ships with several of the DLLs that either Checker or
PatentIn use. Although PatentIn has tried to isolate these DLLs for its
own use, USPTO has been notified by a Checker/PatentIn 3.0 user that one
or both of these products had a problem with Internet Explorer 4.0 on MS
Windows 98. The user quickly isolated the problem and informed USPTO
that an upgrade to Internet Explorer 5.0 eliminated the problem.