**User's Manual**

**for**

**PatentIn 3.3**

Approved by:

Program Manager Date

Prepared by:

Computer Sciences Corporation

2611 Jefferson Davis Highway, Suite 10,000

Arlington, VA 22202-4016

  ----------------------------------- -----------------------------------
  **Document Identification**         

  User's Manual for PatentIn 3.3      PTO-OP-07

  USPTO Contract 50-PBPT-7-00004      System Development and Maintenance

  Task Title                          PatentIn Maintenance

  Task Type                           Discrete

  Task Order Number                   CSC-04-04
  ----------------------------------- -----------------------------------

Version Control Log

+-------------+-------------+-------------+-------------+-------------+
| **Version   | **Date      | **Nature of | **Pages     | **Signature |
| Control     | Change      | Change**    | Affected**  | Authority** |
| Number**    | Effective** |             |             |             |
+-------------+-------------+-------------+-------------+-------------+
| N/A         | 11/10/98    | Initial     | All         | J. Paccassi |
|             |             | document\   |             |             |
|             |             | prepared by |             |             |
|             |             | Lockheed    |             |             |
|             |             | Martin      |             |             |
|             |             | Corporation |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Draft 1.0   | 06/03/99    | Initial     | All         | J. Paccassi |
|             |             | document\   |             |             |
|             |             | prepared by |             |             |
|             |             | CSC         |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 1.0 | 09/16/99    | Incorporate | i, ii, 1v,  | J. Paccassi |
|             |             | USPTO       | 3-5, 3-6,   |             |
|             |             | comments    | 4-2, 4-3,   |             |
|             |             | and updates | 4-5,\       |             |
|             |             | from FQT    | 4-6, 5-2,   |             |
|             |             |             | 5-3,\       |             |
|             |             |             | 5-5, 6-2,   |             |
|             |             |             | 6-4,\       |             |
|             |             |             | 6-7, 7-2,   |             |
|             |             |             | 7-3,\       |             |
|             |             |             | 8-3 through |             |
|             |             |             | 8-9         |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 1.1 | 06/02/00    | Update      | All         | J. Paccassi |
|             |             | document to |             |             |
|             |             | reflect     |             |             |
|             |             | change from |             |             |
|             |             | JAVA to C++ |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 1.2 | 06/22/00    | Incorporate | 3-5, 3-10,  | J. Paccassi |
|             |             | USPTO       | 5-4, 5-10,  |             |
|             |             | updates     | 6-2, 8-4    |             |
|             |             | from FQT    |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 2.0 | 01/26/01    | PatentIn    | All         | J. Paccassi |
|             |             | 3.1 release |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 2.1 | 04/27/01    | Updates to  | All         | J. Paccassi |
|             |             | PatentIn    |             |             |
|             |             | 3.1 release |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 2.2 | 10/16/03    | Updates to  | All         | J. Paccassi |
|             |             | PatentIn    |             |             |
|             |             | 3.2 release |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 2.3 | 03/18/04    | Updates to  | All         | J. Paccassi |
|             |             | PatentIn    |             |             |
|             |             | 3.3 release |             |             |
+-------------+-------------+-------------+-------------+-------------+
| Version 2.4 | 07/30/04    | Updates to  | Figure 5-15 | S. Babil    |
|             |             | PatentIn    | on          |             |
|             |             | 3.3 release |             |             |
|             |             |             | Page 5-16   |             |
+-------------+-------------+-------------+-------------+-------------+

EXECUTIVE SUMMARY

This User's Manual does not conform to the Data Item Description for the
User's Manual, PTO-OP-07. Instead, as required by Section 2.4.4.4 of the
Web PatentIn (WPI) Task Management Plan (TM02), it is being updated
using the format in which the document was originally prepared.

This User's Manual is being updated at United States Patent and
Trademark Office's (USPTO's) direction under task order number CSC-04-04
to include changes for PatentIn 3.3.

TABLE OF CONTENTS

SECTION 1 INTRODUCTION [1-1](#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 3.3 ACCESS
[2-1](#system-requirements-and-patentin-3.3-access)

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

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

SECTION 3 GETTING STARTED [3-1](#getting-started)

3.1 Sequence Screen [3-2](#sequence-screen)

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

3.3 Creating and Saving a New Project
[3-4](#creating-and-saving-a-new-project)

3.4 Opening a project [3-5](#opening-a-project)

3.5 Saving a Project [3-6](#saving-a-project)

3.6 Viewing a Work File [3-7](#viewing-a-work-file)

3.7 Viewing Work in Progress [3-7](#viewing-work-in-progress)

3.8 View a Sequence Listing [3-8](#view-a-sequence-listing)

3.9 Viewing Error Reports [3-9](#viewing-error-reports)

3.10 Rename Sequence [3-10](#rename-sequence)

3.11 Exit PatentIn [3-10](#exit-patentin)

3.12 How to Use Online Help [3-10](#how-to-use-online-help)

3.13 Message Dialog [3-11](#message-dialog)

SECTION 4 PROJECT AND APPLICANT DATA [4-1](#project-and-applicant-data)

4.1 Application Steps Menu [4-2](#application-steps-menu)

4.2 Project Data [4-3](#project-data)

4.3 Prior Application Information [4-3](#prior-application-information)

4.4 Applicant Data [4-5](#applicant-data)

4.4.1 Individual Applicants [4-6](#individual-applicants)

4.4.2 Organization Applicants [4-7](#organization-applicants)

SECTION 5 SEQUENCE DATA [5-1](#sequence-data)

5.1 Sequence [5-2](#sequence)

5.1.1 Selecting a Standard Organism
[5-3](#selecting-a-standard-organism)

5.1.2 Creating default explanations for \"n\"s and \"Xaa\"s
[5-4](#creating-default-explanations-for-ns-and-xaas)

5.1.3 Searching for a Sequence [5-4](#searching-for-a-sequence)

5.1.4 Clearing the Screen [5-4](#clearing-the-screen)

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

5.3 Importing a Sequence [5-6](#importing-a-sequence)

5.3.1 Format for Multi-Sequence Data Files to be Imported by PatentIn
3.x
[5-7](#format-for-multi-sequence-data-files-to-be-imported-by-patentin-3.x)

5.3.1.1 Sequence Header [5-7](#sequence-header)

5.3.1.2 Sequence Data [5-8](#sequence-data-1)

5.3.2 Format for Single Sequence Data Files to be Imported by PatentIn
3.3
[5-8](#format-for-single-sequence-data-files-to-be-imported-by-patentin-3.3)

5.3.3 Importing Sequences from a Project
[5-10](#importing-sequences-from-a-project)

5.3.4 Importing a 2.1 Project [5-11](#importing-a-2.1-project)

5.4 Copying a Sequence [5-12](#copying-a-sequence)

5.5 Pasting a Sequence [5-13](#pasting-a-sequence)

5.6 Deleting a Sequence [5-13](#deleting-a-sequence)

5.7 Skip a Sequence [5-13](#skip-a-sequence)

5.8 Restoring a Sequence [5-14](#restoring-a-sequence)

5.9 Reordering Sequences [5-15](#reordering-sequences)

5.10 Changing a Sequence Type [5-16](#changing-a-sequence-type)

5.11 Validating Sequences [5-16](#validating-sequences)

5.12 Saving Sequences [5-17](#saving-sequences)

5.13 Reloading a Saved Project [5-17](#reloading-a-saved-project)

5.14 Adding Custom Codons [5-17](#adding-custom-codons)

5.15 Adding a Custom Organism [5-18](#adding-a-custom-organism)

5.16 Artificial Sequence or Unknown Organism
[5-20](#artificial-sequence-or-unknown-organism)

SECTION 6 FEATURE DATA [6-1](#feature-data)

6.1 Sequence Features [6-2](#sequence-features)

6.1.1 Feature Key Selection [6-4](#feature-key-selection)

6.1.2 Additional Information Required for Modified_Base
[6-5](#additional-information-required-for-modified_base)

6.1.3 Additional Information on CDS
[6-5](#additional-information-on-cds)

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

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

6.1.6 Additional Information for MOD_RES
[6-7](#additional-information-for-mod_res)

SECTION 7 PUBLICATION DATA [7-1](#publication-data)

7.1 Publication Type Screen [7-2](#publication-type-screen)

7.2 Journals Publication Information
[7-3](#journals-publication-information)

7.3 Databases Publication Information
[7-5](#databases-publication-information)

7.4 Patents Publications Information
[7-6](#patents-publications-information)

7.5 Theses Publication Information
[7-8](#theses-publication-information)

SECTION 8 CREATING A SEQUENCE LISTING PROJECT FILE
[8-1](#creating-a-sequence-listing-project-file)

8.1 Sequence Listing File [8-2](#sequence-listing-file)

8.2 Generating a Sequence Listing File
[8-2](#generating-a-sequence-listing-file)

8.3 Viewing a Sequence Listing File
[8-4](#viewing-a-sequence-listing-file)

8.4 Copying the Sequence Listing to a disk
[8-5](#copying-the-sequence-listing-to-a-disk)

Appendix A LIST OF ACRONYMS [A-1](#list-of-acronyms)

Appendix B FIELD IDENTIFIERS, LENGTHS AND TYPES
[B-1](#field-identifiers-lengths-and-types)

Appendix C COUNTRY CODES [C-1](#country-codes)

Appendix D CONVERSION TABLE BETWEEN NUCLEOTIDE TRIPLETS (CODONS) AND
ONE- AND THREE-LETTER AMINO ACID CODES
[D-1](#conversion-table-between-nucleotide-triplets-codons-and-one--and-three-letter-amino-acid-codes)

Appendix E NUCLEOTIDE SEQUENCE FEATURES
[E-1](#nucleotide-sequence-features)

Appendix F AMINO ACID SEQUENCE FEATURES
[F-1](#amino-acid-sequence-features)

Appendix G DATA TABLES FOR MOD_RES SEQUENCE FEATURES
[G-1](#data-tables-for-mod_res-sequence-features)

Appendix H ADDITIONAL LIPID SEQUENCE FEATURES
[H-1](#additional-lipid-sequence-features)

Appendix I ACCEPTABLE CHARACTERS IN THE SEQUENCE DESCRIPTION FIELD
[I-1](#acceptable-characters-in-the-sequence-description-field)

Appendix J ADDITIONAL MODIFIED_BASE SEQUENCE FEATURES
[J-1](#additional-modified_base-sequence-features)

Appendix K TECHNICAL NOTES [K-1](#technical-notes)

K.1 Microsoft® Access Notes [K-2](#__RefHeading___Toc67224342)

K.2 General Hints and Tips [K-3](#__RefHeading___Toc67224343)

K.3 installation and testing notes [K-3](#__RefHeading___Toc67224344)

LIST OF TABLES

Table 1‑1: Document Conventions [1-2](#__RefHeading___Toc53473318)

Table 5‑1: Header for Sequence [5-7](#__RefHeading___Toc53473319)

Table B‑1: Field Name, Identifier, Size, and Type
[B-2](#__RefHeading___Toc53473320)

Table C‑1: Country Codes [C-2](#__RefHeading___Toc53473321)

Table D‑1: Exchange Nucleotide Characters and Amino Characters
[D-2](#__RefHeading___Toc53473322)

Table E‑1: Nucleotide Sequence Features
[E-2](#__RefHeading___Toc53473323)

Table F‑1: Amino Acid Sequence Features
[F-2](#__RefHeading___Toc53473324)

Table G‑1: First Data Table for MOD_RES Sequence Features
[G-2](#__RefHeading___Toc53473325)

Table G‑2: Second Data Table for MOD_RES Sequences
[G-2](#__RefHeading___Toc53473326)

Table H‑1: Additional Lipid Sequence Features
[H-2](#__RefHeading___Toc53473327)

Table I‑1: Acceptable Characters in the Sequence Description Field
[I-2](#__RefHeading___Toc53473328)

Table J‑1: Modified_base Sequence Features
[J-2](#__RefHeading___Toc53473329)

LIST OF FIGURES

Figure 3‑1: Sequence Screen [3-2](#__RefHeading___Toc67224978)

Figure 3‑2: Project Menu [3-3](#__RefHeading___Toc67224979)

Figure 3‑3: Save As Screen [3-4](#__RefHeading___Toc67224980)

Figure 3‑4: Open Screen [3-5](#__RefHeading___Toc67224981)

Figure 3‑5: Save As Screen [3-6](#__RefHeading___Toc67224982)

Figure 3‑6: View Work in Progress Window
[3-7](#__RefHeading___Toc67224983)

Figure 3‑7: View Sequence Listing Window
[3-8](#__RefHeading___Toc67224984)

Figure 3‑8: View Error Report Window [3-9](#__RefHeading___Toc67224985)

Figure 3‑9: Rename Sequence Screen [3-10](#_Ref502035959)

Figure 3‑10: Exit PatentIn Screen [3-10](#__RefHeading___Toc67224987)

Figure 3‑11: Help Screen [3-11](#__RefHeading___Toc67224988)

Figure 3‑12: Message Dialog Screen [3-11](#__RefHeading___Toc67224989)

Figure 4‑1: Application Steps Menu [4-2](#__RefHeading___Toc67224990)

Figure 4‑2: Project Data Screen [4-3](#__RefHeading___Toc67224991)

Figure 4‑3: Prior Application Information Screen
[4-4](#__RefHeading___Toc67224992)

Figure 4‑4: Applicant Data Screen [4-5](#_Ref476730233)

Figure 4‑5: Individual Applicants Screen
[4-6](#__RefHeading___Toc67224994)

Figure 4‑6: Organization Applicants Screen
[4-8](#__RefHeading___Toc67224995)

Figure 5‑1: Sequence Screen [5-2](#__RefHeading___Toc67224996)

Figure 5‑2: Selecting an Organism Screen
[5-3](#__RefHeading___Toc67224997)

Figure 5‑3: Add A Sequence Screen [5-5](#__RefHeading___Toc67224998)

Figure 5‑4: Import Sequence(s) Screen [5-6](#__RefHeading___Toc67224999)

Figure 5‑5: Sample ASCII Sequence Data
[5-8](#__RefHeading___Toc67225000)

Figure 5‑6: Sequence Type Selection Screen
[5-8](#__RefHeading___Toc67225001)

Figure 5‑7: Sequences Being Imported Screen
[5-9](#__RefHeading___Toc67225002)

Figure 5‑8: Validation Errors Screen [5-10](#__RefHeading___Toc67225003)

Figure 5‑9: Select Sequences From Project Screen
[5-11](#__RefHeading___Toc67225004)

Figure 5‑10: Browse Window for 2.1 Project Import
[5-12](#__RefHeading___Toc67225005)

Figure 5‑11: PatentIn 2.1 Projects List
[5-12](#__RefHeading___Toc67225006)

Figure 5‑12: Edit Menu [5-13](#__RefHeading___Toc67225007)

Figure 5‑13: Sequence Recovery Screen
[5-14](#__RefHeading___Toc67225008)

Figure 5‑14: Reorder Sequences Screen
[5-15](#__RefHeading___Toc67225009)

Figure 5‑15: Change Sequence Type Screen
[5-16](#__RefHeading___Toc67225010)

Figure 5‑16: Custom Codons Input Screen
[5-17](#__RefHeading___Toc67225011)

Figure 5‑17: Amino Acid Drop Down List Screen
[5-18](#__RefHeading___Toc67225012)

Figure 5‑18: Custom Organism Input Screen
[5-19](#__RefHeading___Toc67225013)

Figure 5‑19: Artificial Sequence/Unknown Organism Comment
[5-20](#__RefHeading___Toc67225014)

Figure 6‑1: Features Screen [6-2](#__RefHeading___Toc67225015)

Figure 6‑2: Feature Names/Key Selection Screen
[6-4](#__RefHeading___Toc67225016)

Figure 6‑3: Feature Names/Key Selection Screen with Modified Base
[6-5](#__RefHeading___Toc67225017)

Figure 6‑4: Feature Names/Key Selection Screen with LIPID Selected
[6-6](#__RefHeading___Toc67225018)

Figure 6‑5: Feature Names/Key Selection Screen with MOD_RES Selected
[6-7](#__RefHeading___Toc67225019)

Figure 6‑6: First MOD_RES Pull Down List
[6-8](#__RefHeading___Toc67225020)

Figure 6‑7: Second MOD_RES Pull Down List
[6-9](#__RefHeading___Toc67225021)

Figure 7‑1: Publication Type Screen [7-2](#__RefHeading___Toc67225022)

Figure 7‑2: Journals Publication Information Screen
[7-3](#_Ref476978663)

Figure 7‑3: Databases Publication Information Screen
[7-5](#__RefHeading___Toc67225024)

Figure 7‑4: Patents Publication Information Screen
[7-6](#__RefHeading___Toc67225025)

Figure 7‑5: Theses Publications Information Screen
[7-8](#__RefHeading___Toc67225026)

Figure 8‑1: Sequence Generation Screen
[8-2](#__RefHeading___Toc67225027)

Figure 8‑2: Second Sequence Generation Screen
[8-3](#__RefHeading___Toc67225028)

Figure 8‑3: View Results Window [8-4](#__RefHeading___Toc67225029)

Figure 8‑4: Copy to Disk Screen [8-5](#__RefHeading___Toc67225030)

#  INTRODUCTION

SECTION 1\
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 below.

[]{#__RefHeading___Toc53473318 .anchor}Table 1‑1: Document Conventions

  ----------------------------------------------------------------------------------------------------------------------------------------
  **Notation**                                          **Represents**               **Example**
  ----------------------------------------------------- ---------------------------- -----------------------------------------------------
                                                        Process the command with a   Select Open from the file menu.
                                                        mouse action.                

                                                        Process the command with the Enter changes into the Edit field.
                                                        keyboard.                    

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

  ![](media/image3.wmf){width="0.22916666666666666in"   An informative message to    ![](media/image3.wmf){width="0.21388888888888888in"
  height="0.28541666666666665in"}                       the user.                    height="0.2638888888888889in"} NOTE: These fields are
                                                                                     mandatory.
  ----------------------------------------------------------------------------------------------------------------------------------------

## 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
U.S. final rule, \"Requirements for Patent Applications Containing
Nucleotide Sequence and/or Amino Acid Disclosures.\" It runs on Windows
95, Windows 98, Windows NT, Windows 2000 and Windows XP. Screen displays
are in English. Since the sequence listings generated by PatentIn are in
compliance with ST.25, this program has worldwide applicability.

For ease of use, the design follows 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 sequence listing 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 3.3 ACCESS

SECTION 2\
system requirEments and PATENTIN 3.3 Access

## System Requirements

PatentIn is a self-contained application that can be downloaded from the
USPTO web site. It operates in a Windows 95/98/NT/2000/XP environment. A
minimum of 64 Megabytes (MB) of memory is recommended. Additional memory
may be required for large patent applications. Very large projects,
projects with 100,000 sequences or a sequence approaching 1M, will need
a minimum of 128 MB of memory. The disk space required to install
PatentIn 3.3 is about 6 MB. Additional disk space is required to store
project files and sequence listing files. Microsoft® Access 97, with
some of the extensions, is required to use the PatentIn 2.1 project load
feature. (The load of the sequence data files does not have this
restriction.)

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.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [Special Note for users with very large
sequences and large numbers of sequences]{.smallcaps}: PTO has located a
viewer that works 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 2000 SR-1. PTO was able to successfully
open files of 60MB and 120 MB. The viewer was tested on a laptop with
Windows 98. (LocalAdmin may be required for installation.)

## PatentIn Access

PatentIn was designed to be installed on individual computers. It can be
downloaded onto your personal computer 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/\
patentin33rel.htm](http://www.uspto.gov/web/offices/pac/patin/patentin33rel.htm).
Before the installation of PatentIn 3.3, be sure to close all running
applications on your computer and then follow the instructions found on
the Web page to download PatentIn 3.3 and install it on your PC. Upon
completing the installation, an icon will be placed on your desktop.
Access to the PatentIn 3.3 application program occurs when you
double-click on the PatentIn 3.3 icon.

#  GETTING STARTED

SECTION 3\
getting starteD

##  Sequence Screen

When you first access PatentIn by double-clicking on the PatentIn 3.3
icon on your desktop, you have immediate access to the Sequence Screen.

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

![](media/image4.wmf)

[]{#__RefHeading___Toc67224978 .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^®^ Windows-type
menus. The user may select any one of the three drop-down menus when a
project is begun. 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 3-3) where a new
project is given a name and is saved. Selecting "Open" displays the Open
Screen (Figure 3-4) where the user can select a previously saved project
to open. The " Exit PatentIn 3.3" 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 (Figure 3-2) selections are shown below. 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/image6.png){width="6.5in" height="4.748611111111111in"}

[]{#__RefHeading___Toc67224979 .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:

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/image7.png){width="4.457638888888889in"
height="2.845833333333333in"}

[]{#__RefHeading___Toc67224980 .anchor}Figure 3‑3: Save As Screen

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [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. The generated
listing is saved with the same file name as the project and has the
extension "ST25.txt".

## 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/image8.png){width="4.457638888888889in"
height="2.845833333333333in"}

[]{#__RefHeading___Toc67224981 .anchor}Figure 3‑4: Open Screen

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [Special Note for users with very large
sequences and/OR large numbers of sequences:]{.smallcaps} 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:

```{=html}
<!-- -->
```
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/image9.png){width="4.457638888888889in"
height="2.845833333333333in"}

[]{#__RefHeading___Toc67224982 .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**.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} This work file was
built by selecting **Create Work File**.

## Viewing Work in Progress

PatentIn provides the user with an on-screen display of the Patent
Application with the View Work in Progress Window (Figure 3-6).

![](media/image10.png){width="6.497916666666667in"
height="4.639583333333333in"}

[]{#__RefHeading___Toc67224983 .anchor}Figure 3‑6: View Work in Progress
Window

To view the current patent application:

1.  From the Project menu, select **View**, **Work in Progress**.

```{=html}
<!-- -->
```
13. To print the error 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 View Sequence Listing Window (Figure 3-7).

![](media/image11.png){width="6.497916666666667in"
height="4.639583333333333in"}

[]{#__RefHeading___Toc67224984 .anchor}Figure 3‑7: View Sequence Listing
Window

To view the sequence listing:

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

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

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

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} The sequence must
first be generated.

## Viewing Error Reports

PatentIn provides the user with an on-screen Error Report with the View
Error Report Window (Figure 3-8), if one exists, for the opened project.

![](media/image12.png){width="6.497916666666667in"
height="4.639583333333333in"}

[]{#__RefHeading___Toc67224985 .anchor}Figure 3‑8: View Error Report
Window

To view an error report:

1.  From the **Project** menu, select **View 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 (Figure 3-9).

![](media/image13.png){width="2.970833333333333in"
height="1.945138888888889in"}

[]{#_Ref502035959 .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 Exit PatentIn Screen (Figure 3-10) about whether the project
should be saved:

![](media/image14.png){width="2.7784722222222222in" height="1.31875in"}

[]{#__RefHeading___Toc67224987 .anchor}Figure 3‑10: Exit PatentIn Screen

## How to Use Online Help

On-line help is available for most of the PatentIn screens. The Help
Screen (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 (Figure 3-1).

![](media/image15.png){width="5.957638888888889in"
height="4.692361111111111in"}

[]{#__RefHeading___Toc67224988 .anchor}Figure 3‑11: Help Screen

1.  To exit the **Help** screen, click on the **OK** button.

## Message Dialog 

The Message Dialog Screen (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/image16.png){width="2.4868055555555557in" height="1.31875in"}

[]{#__RefHeading___Toc67224989 .anchor}Figure 3‑12: Message Dialog
Screen

#  PROJECT AND APPLICANT DATA

Section 4\
Project and Applicant 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 begun, has been created or selected. The project name is
visible at the upper left corner of the screen. In this example the user
has opened a previously existing project called New Name.

![](media/image17.png){width="6.5in" height="4.748611111111111in"}

[]{#__RefHeading___Toc67224990 .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.

![](media/image3.wmf){width="0.21875in" height="0.21805555555555556in"}
[NOTE:]{.smallcaps} The mandatory information fields (Title Of Invention
and Application File Reference) are in red.

![](media/image18.png){width="6.432638888888889in"
height="3.8048611111111112in"}

[]{#__RefHeading___Toc67224991 .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**.

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 4-3). They will be
displayed in the table in the order entered and may be selected for
editing or deleting.

![](media/image19.png){width="6.0569444444444445in"
height="4.6090277777777775in"}

[]{#__RefHeading___Toc67224992 .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.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [New to PatentIn:]{.smallcaps} In
[PatentIn 3.3, w]{.smallcaps}hen **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 Applicant 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/image20.png){width="6.5in" height="4.748611111111111in"}

[]{#_Ref476730233 .anchor}

Figure 4‑16: Applicant 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.

![](media/image3.wmf){width="0.21875in" height="0.21805555555555556in"}
[NOTE:]{.smallcaps} The field names in red (Last Name and First Name)
are mandatory information.

![](media/image21.png){width="6.055555555555555in"
height="5.207638888888889in"}

[]{#__RefHeading___Toc67224994 .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, 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.

    ![](media/image3.wmf){width="0.22916666666666666in"
    height="0.28541666666666665in"} [NOTE:]{.smallcaps} The phone
    number, fax number and zip code are no longer validated.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [New to PatentIn:]{.smallcaps} In
[PatentIn 3.3, w]{.smallcaps}hen **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.

![](media/image22.png){width="6.0569444444444445in"
height="4.7756944444444445in"}

[]{#__RefHeading___Toc67224995 .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, 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 9 until all applicant information has been
    included.

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

    ![](media/image3.wmf){width="0.22916666666666666in"
    height="0.28541666666666665in"} [NOTE:]{.smallcaps} The phone
    number, fax number and zip code are no longer validated.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [New to PatentIn:]{.smallcaps} In
[PatentIn 3.3, w]{.smallcaps}hen **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

Section 5\
Sequence Data

## Sequence

The Sequence Screen (Figure 5-19) 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/image23.png){width="6.5in" height="4.748611111111111in"}

[]{#__RefHeading___Toc67224996 .anchor}Figure 5‑19: Sequence Screen

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} To begin entering a
new sequence you must first have a sequence name. See Section 5.2.

To select a sequence for editing:

Select a sequence name from the list of sequences.

The following sequence characteristics are displayed:

**Cursor Pos -** 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

This screen, 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/image24.png){width="6.082638888888889in"
height="4.832638888888889in"}

[]{#__RefHeading___Toc67224997 .anchor}Figure 5‑20: Selecting an
Organism Screen

**To select an Organism Name:**

1.  Click on the **Standard** button (Figure 5-19)

```{=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.

### Creating default explanations for \"n\"s and \"Xaa\"s

PatentIn 3.3 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 (Figure 5-19) 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 3.3 will create any missing
misc_features. Users may create selected definitions by hand and
PatentIn 3.3 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 edit
    field below the **Search** **for** button (Figure 5-19).

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

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} Each
[s]{.smallcaps}earch is limited/truncated to 60 characters.

### Clearing the Screen

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

## Adding a Sequence

The **Add** button on the Sequence Screen (Figure 5-19) provides a means
to enter a sequence name and to select a sequence type from a list of
radio buttons (Figure 5-21).

![](media/image25.png){width="2.6791666666666667in"
height="3.609722222222222in"}

[]{#__RefHeading___Toc67224998 .anchor}Figure 5‑21: Add A Sequence
Screen

To add a sequence:

1.  From the Sequence Screen, select the **Add** button. The Add A
    Sequence Screen appears (Figure 5-21)

```{=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 95, a maximum of 64K characters
will display in the field. In Windows NT, 98, 2000 and XP, the upper
limit is over 1 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 (Figure 5-19) provides a
means to import sequences from either a file, a project, or a 2.1
project by selecting one of three radio buttons.

![](media/image26.png){width="6.388194444444444in"
height="2.7909722222222224in"}

[]{#__RefHeading___Toc67224999 .anchor}Figure 5‑22: Import Sequence(s)
Screen

1.  To use a sequence from a 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 use a sequence 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 use a project from a PatentIn 2.1, click on the **Import** button
    on the Sequence Screen, and then click on the **2.1 Project** 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. Unchecking 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.x 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. For best results it is
    recommended that the sequence files contain only the sequence, with
    spaces and numbering, and that any title or other text be deleted
    prior to importing. For example, if the title of the sequence is
    Genomic Deoxyribonucleic Acid (DNA), PatentIn 3.3 would filter out
    the characters e, o and i and so the first seven characters of your
    sequence would be "gnmcdna".

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} Importation of a 2.1
Project requires additional software to be installed. See section 5.3.4.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} 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 D: 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 to be Imported by PatentIn 3.x

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 5-2).

\<*SequenceName;SequenceType;OrganismName*\>

[]{#__RefHeading___Toc53473319 .anchor}Table 5‑2: Header for Sequence

+-----------------------------------+-----------------------------------+
| *SequenceName*                    | 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, and is  |
|                                   | optional. If it is omitted, the   |
|                                   | header looks like:                |
|                                   | \<*SequenceName;SequenceType*;\>. |
+-----------------------------------+-----------------------------------+

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} 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
(Figure 5-23):

\< First Sequence;DNA;Abies alba\>

ttttcttattgtttctcctactgcttatcataatgattgtcgtagtggcttcctcatcgt

ctcccccaccgcctaccacaacgactgccgcagcggattactaatagtatcaccaacagc

ataacaaaaagaatgacgaagagggttgctgatggtgtcgccgacggcgtagcagaagga

gtggcggagggg

\< Second Sequence;RNA; \>

uuuucuuauuguuucuccuacugcuuaucauaaugauugucguaguggcuuccucaucgu

cucccccaccgccuaccacaacgacugccgcagcggauuacuaauaguaucaccaacagc

auaacaaaaagaaugacgaagaggguugcugauggugucgccgacggcguagcagaagga

guggcggagggg

[]{#__RefHeading___Toc67225000 .anchor}Figure 5‑23: Sample ASCII
Sequence Data

### Format for Single Sequence Data Files to be Imported by PatentIn 3.3

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 (Figure
5-24) and the file is assumed to be a single sequence data file.

![](media/image27.png){width="2.970833333333333in"
height="2.2083333333333335in"}

[]{#__RefHeading___Toc67225001 .anchor}Figure 5‑24: Sequence Type
Selection Screen

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} PatentIn 2.1 ASCII
text files used the extension ".gbs" for its sequence files.

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

![](media/image28.png){width="2.970833333333333in"
height="1.945138888888889in"}

[]{#__RefHeading___Toc67225002 .anchor}Figure 5‑25: Sequences Being
Imported Screen

A Validation Errors screen is displayed if validation errors occur. In
the next example (Figure 5‑8), the file singlefilenoheader was specified
as DNA instead of Protein 1. Nucleo is actually a file with the names of
nucleotides, not the sequences.

![](media/image29.png){width="5.707638888888889in"
height="4.847222222222222in"}

[]{#__RefHeading___Toc67225003 .anchor}Figure 5‑26: Validation Errors
Screen

### Importing Sequences from a Project

PatentIn provides a mechanism to import sequences from a PatentIn 3.x
project (Figure 5-22: Import Sequence(s) Screen).

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.

    ![](media/image3.wmf){width="0.22916666666666666in"
    height="0.28541666666666665in"} [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/image30.png){width="5.555555555555555in" height="5.18125in"}

[]{#__RefHeading___Toc67225004 .anchor}Figure 5‑27: Select Sequences
From Project Screen

### Importing a 2.1 Project

1.  To use a sequence from a PatentIn 2.1 project file, click on the
    **Import** button on the sequence screen, then click on the **2.1
    Project** radio button.

```{=html}
<!-- -->
```
68. The **Browse** button is provided to assist the user in providing
    the file folder and file name. Notice that in this case a ".dbf"
    file is selected, not a project or text file. See Figure 5-28.

> ![](media/image31.png){width="4.458333333333333in"
> height="2.8465277777777778in"}

[]{#__RefHeading___Toc67225005 .anchor}Figure 5‑28: Browse Window for
2.1 Project Import

69. After the PatentIn 2.1 Project file is identified, the list of
    project long names is displayed. See Figure 5-29.

![](media/image32.png){width="3.0277777777777777in"
height="2.7368055555555557in"}

[]{#__RefHeading___Toc67225006 .anchor}Figure 5‑29: PatentIn 2.1
Projects List

70. Click on the project to be imported.

71. Click on the **OK** button.

## Copying a Sequence

PatentIn uses standard Windows-type edit features.

To copy a sequence:

1.  Highlight the sequence to be copied.

```{=html}
<!-- -->
```
72. Click on the **Edit** menu, then click **Copy** (Figure 5-30).

![](media/image33.png){width="6.5in" height="4.748611111111111in"}

[]{#__RefHeading___Toc67225007 .anchor}Figure 5‑30: Edit Menu

## Pasting a Sequence

To paste a sequence:

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

```{=html}
<!-- -->
```
73. Click on the **Edit**, 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 3.3 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}
<!-- -->
```
74. Click on the **Skip this sequence** checkbox to turn on the skip
    sequence flag on the Sequence Screen (Figure 5-19). PatentIn 3.3
    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:

75. Click on the **Restore** button on the main screen. The Sequence
    Recovery Screen (Figure 5-31) appears.

76. Select the sequence(s) to be restored.

77. Click on the **Restore** button.

![](media/image34.png){width="3.8743055555555554in"
height="4.915972222222222in"}

[]{#__RefHeading___Toc67225008 .anchor}Figure 5‑31: Sequence Recovery
Screen

## Reordering Sequences

The Reorder Sequences Screen (Figure 5-32) 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/image35.png){width="6.429861111111111in"
height="4.915972222222222in"}

[]{#__RefHeading___Toc67225009 .anchor}Figure 5‑32: Reorder Sequences
Screen

To reorder sequences:

1.  Select the sequence row(s) from the menu on the left-hand side.

```{=html}
<!-- -->
```
78. Click on the row the sequence will follow on the right-hand side.

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

## Changing a Sequence Type

The **AlterSeqType** button on the Sequence Screen (Figure 5-19)
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 below.

![](media/image36.png){width="2.8180555555555555in"
height="3.4298611111111112in"}

[]{#__RefHeading___Toc67225010 .anchor}Figure 5‑33: 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}
<!-- -->
```
80. Click on the **AlterSeqType** button. The Change Sequence Type
    screen appears.

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

82. 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 (Figure 5-19), click on the **Validate**
    button. A message screen will inform you if there was an error,
    otherwise Validation OK will appear on the status bar.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} 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.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} 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 5-34) 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/image37.png){width="5.638888888888889in"
height="4.472222222222222in"}

[]{#__RefHeading___Toc67225011 .anchor}Figure 5‑34: Custom Codons Input
Screen

To add a Custom Codon:

1.  Select the **Define Custom Codons** item from the **Application**
    **Steps** menu (Figure 4-13).

```{=html}
<!-- -->
```
83. Select an **Amino Acid** from the drop-down list (Figure 5-35).

84. Enter the **Custom Codon**.

85. Click on the **Insert** button.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [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}
<!-- -->
```
86. Click on the **Delete** button.

![](media/image38.png){width="5.638888888888889in"
height="4.472222222222222in"}

[]{#__RefHeading___Toc67225012 .anchor}Figure 5‑35: Amino Acid Drop Down
List Screen

## Adding a Custom Organism

The Custom Organism Input Screen (Figure 5-36) 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/image39.png){width="4.624305555555556in"
height="4.6819444444444445in"}

[]{#__RefHeading___Toc67225013 .anchor}Figure 5‑36: Custom Organism
Input Screen

To add a Custom Organism:

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

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

88. Click on the **Insert** button.

    To delete a Custom Organism:

```{=html}
<!-- -->
```
1.  Click on the Custom Organism in the list.

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

    To replace a Custom Organism:

```{=html}
<!-- -->
```
1.  Click on the Custom Organism in the list.

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

91. Click on the **Replace** button.

    To enter a Custom Organism on the Sequence screen:

```{=html}
<!-- -->
```
1.  Select the Organism so that the name appears in the "Please enter a
    custom organism name:" box.

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

    To apply a Custom Organism to all of the Sequences in the Project:

```{=html}
<!-- -->
```
1.  Click the check box marked: **Apply to all Sequences in the
    Project**.

```{=html}
<!-- -->
```
93. 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.

![](media/image40.png){width="4.6506944444444445in"
height="2.2645833333333334in"}

[]{#__RefHeading___Toc67225014 .anchor}Figure 5‑37: Artificial
Sequence/Unknown Organism Comment

1.  Select the **Standard** button from the Sequence Screen (Figure
    5-19).

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

95. Tab or move to another cell. The comment box, Figure 5-37, will
    automatically pop-up when a definition of the organism is required.

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

97. 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 way 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.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} This field can also
be accessed by choosing Application Steps \| Artificial Sequence/Unknown
Comment (Figure 4-13).

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} The content of this
box should be as descriptive as possible while remaining as terse as
possible.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [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 3.3 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 

Section 6\
Feature Data

## Sequence Features 

The Features Screen (Figure 6-38) 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/image41.png){width="6.1819444444444445in"
height="5.097916666666666in"}

[]{#__RefHeading___Toc67225015 .anchor}Figure 6‑38: Features Screen

To enter information about a Feature:

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

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

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

100. 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.

101. To clear the **Edit Feature** portion of the screen Click on the
     **Clear** button.

102. To insert an entry from the **Feature List**, highlight it and
     click on the **Insert** button.

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

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

105. 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.

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

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

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

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

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} The **Join All
CDSs** disappears and appears based on whether there is more than one
CDS in the Feature List.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [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.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [New to PatentIn:]{.smallcaps} In
PatentIn 3.3 there is an automatic expansion of the possible resolutions
for "Xaa."

### Feature Key Selection

The Feature Names/Key Selection Screen (Figure 6-39) allows the user to
select a Nucleotide name.

![](media/image42.png){width="5.613888888888889in"
height="4.5256944444444445in"}

[]{#__RefHeading___Toc67225016 .anchor}Figure 6‑39: Feature Names/Key
Selection Screen

To select a Nucleotide name:

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

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

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

111. Click on **OK** to accept the selection and return to the Features
     Screen (Figure 6--1).

### Additional Information Required for Modified_Base

The Feature Names/Key Selection Screen (Figure 6-40) automatically
reveals an additional window when modified_base is selected.

![](media/image43.png){width="5.915972222222222in" height="5.43125in"}

[]{#__RefHeading___Toc67225017 .anchor}Figure 6‑40: 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."

```{=html}
<!-- -->
```
112. Select modified_base from the list (Figure 6-40).

113. Click on **OK** (Figure 6-39).

### Additional Information on CDS

When a Coding Sequence 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 3.3 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 Names/Key Selection Screen (Figure 6-4) automatically
reveals an additional window when LIPID is selected.

![](media/image44.png){width="5.613888888888889in"
height="4.5256944444444445in"}

[]{#__RefHeading___Toc67225018 .anchor}Figure 6‑41: Feature Names/Key
Selection Screen with LIPID Selected

To select an Amino Acid name:

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

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

```{=html}
<!-- -->
```
114. Click on the down arrow to open the drop down list (Figure 6‑5);
     select a name from the list.

115. Click on **OK** to accept the selection and return to the Features
     Screen, (Figure 6-4).

     To add information about a LIPID:

```{=html}
<!-- -->
```
1.  Select the pull down arrow on the box marked **Add the following
    LIPID to the Other Information**.

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

117. Click on **OK** (Figure 6-4).

### Additional Information for MOD_RES

The Feature Names/Key Selection Screen (Figure 6-42) automatically
reveals an additional two windows when MOD_RES is selected.

![](media/image45.png){width="5.613888888888889in"
height="4.5256944444444445in"}

[]{#__RefHeading___Toc67225019 .anchor}Figure 6‑42: Feature Names/Key
Selection Screen with MOD_RES Selected

To select an Amino Acid name:

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

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

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

```{=html}
<!-- -->
```
118. 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}
<!-- -->
```
119. Select the appropriate information from the list (Figure 6-6).

120. Click on **OK** (Figure 6-42).

![](media/image46.png){width="5.613888888888889in"
height="4.5256944444444445in"}

[]{#__RefHeading___Toc67225020 .anchor}Figure 6‑43: First MOD_RES Pull
Down List

121. 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 6-44).

```{=html}
<!-- -->
```
6.  Click on **OK** (Figure 6-42).

![](media/image47.png){width="5.999305555555556in"
height="5.207638888888889in"}

[]{#__RefHeading___Toc67225021 .anchor}Figure 6‑44: Second MOD_RES Pull
Down List

#  PUBLICATION DATA

Section 7\
Publication Data

## Publication Type Screen 

The Publication Type Screen (Figure 7-45) 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/image48.png){width="6.5in" height="4.748611111111111in"}

[]{#__RefHeading___Toc67225022 .anchor}Figure 7‑45: 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 Publication Information Screen (Figure 7-46) provides the
user with a means to input published supporting scientific literature
with the patent application.

[]{#_Ref476978663
.anchor}![](media/image49.png){width="6.098611111111111in"
height="5.55625in"}

Figure 7‑46: 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. In the 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 7-47) provides the
user with a means to input published supporting scientific database with
the patent application.

![](media/image50.png){width="6.138888888888889in"
height="5.040972222222222in"}

[]{#__RefHeading___Toc67225024 .anchor}Figure 7‑47: 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**, and 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 7-48) provides the
user with a means to input published supporting patent publication
information with the patent application.

![](media/image51.png){width="6.432638888888889in"
height="5.499305555555556in"}

[]{#__RefHeading___Toc67225025 .anchor}Figure 7‑48: Patents Publication
Information Screen

To enter information about a Patent Publication:

1.  From the **Application Steps** select **Publications Data**, 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 Publications Information Screen (Figure 7-49) provides the
user with a means to input published supporting thesis publication
information with the patent application.

![](media/image52.png){width="6.180555555555555in"
height="5.316666666666666in"}

[]{#__RefHeading___Toc67225026 .anchor}Figure 7‑49: Theses Publications
Information Screen

To enter information about a Thesis Publication:

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

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

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

4.  Enter the **Author Name**.

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

SECTION 8\
Creating a Sequence Listing File

## Sequence Listing File

The sequence listing file includes all the information required by
ST.25. PatentIn 3.3 will generate a sequence listing with the extension
"ST25.txt" appended to the project name. This ST25 file is placed in the
directory containing the project.

## Generating a Sequence Listing File

The Sequence Generation Screen (Figure 8-50) 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/image53.png){width="6.502083333333333in"
height="2.152083333333333in"}

[]{#__RefHeading___Toc67225027 .anchor}Figure 8‑50: Sequence Generation
Screen

To Generate a Sequence Listing:

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

```{=html}
<!-- -->
```
2.  Click in the box next to "Pause after each error message" 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.

![](media/image54.png){width="6.502083333333333in"
height="2.152083333333333in"}

[]{#__RefHeading___Toc67225028 .anchor}Figure 8‑51: Second Sequence
Generation Screen

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.

## 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 8-52). If
    **View** **listing or error log when done** was not selected, you
    can view the same results by selecting **View Sequence Listing**
    from the **Project** menu.

![](media/image55.png){width="6.497916666666667in"
height="4.639583333333333in"}

[]{#__RefHeading___Toc67225029 .anchor}Figure 8‑52: View Results Window

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [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 2000 SR-1. PTO successfully viewed 60MB and
120MB files. It should manage files of almost any size. It was tested on
a laptop with Windows 98 (LocalAdmin may be required for installation).
The United States Patent and Trademark Office 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 8-53) 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/image56.png){width="4.457638888888889in"
height="2.845833333333333in"}

[]{#__RefHeading___Toc67225030 .anchor}Figure 8‑53: Copy to Disk Screen

To copy a sequence listing:

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

```{=html}
<!-- -->
```
122. Select a drive name (Figure 8-53) in the Save in field.

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

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

125. 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**.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} NOTE: .zip works only with floppy
disk(s) and will format the disk before writing anything to the disk.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} In general, if a
hard drive is selected, the user will be prompted to select a removable
medium as the target for this copy.

![](media/image3.wmf){width="0.22916666666666666in"
height="0.28541666666666665in"} [NOTE:]{.smallcaps} The save to a 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

APPENDIX A\
LIST OF ACRONYMS

ASCII American Standard Code for Information Interchange

CDS CoDing Sequence

CSC Computer Sciences Corporation

DNA Deoxyriboneucleic Acid

FQT Functional Qualification Test

MB Megabytes

MHz Megahertz

PC Personal Computer

PTO Patent and Trademark Office

RNA Riboneucleic Acid

scRNA small cytoplasmic RNA

TM02 Task Management Plan

USPTO United States Patent and Trademark Office

WIPO World Intellectual Property Organization

WPI Web PatentIn

#########  FIELD IDENTIFIERS, LENGTHS AND TYPES

APPENDIX B\
FIELD IDENTIFIERS, LENGTHS AND TYPES

Table B-1, below, 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___Toc53473320 .anchor}Table B‑3: 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

APPENDIX C\
COUNTRY CODES

Table C-1 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___Toc53473321 .anchor}Table C‑4: 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

APPENDIX D\
CONVERSION TABLE BETWEEN NUCLEOTIDE TRIPLETS (CODONS) AND ONE- AND
THREE-LETTER AMINO ACID CODES

Table D-1 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___Toc53473322 .anchor}Table D‑5: 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

APPENDIX E\
NUCLEOTIDE SEQUENCE FEATURES

Table E-1 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___Toc53473323 .anchor}Table E‑6: 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)                                        |
+---------------+------------------------------------------------------+
| mi            | feature sequence is different from that presented in |
| sc_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)                          |
+---------------+------------------------------------------------------+
| m             | any secondary or tertiary structure or conformation  |
| isc_structure | that cannot be described by other Structure keys     |
|               | (stem_loop and D-loop)                               |
+---------------+------------------------------------------------------+
| modified_base | the indicated nucleotide is a modified nucleotide    |
|               | and 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                                      |
+---------------+------------------------------------------------------+
| precursor_RNA | any RNA species that is not yet the mature 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)                                            |
+---------------+------------------------------------------------------+
| pr            | primary (initial, unprocessed) transcript; includes  |
| im_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                                |
+---------------+------------------------------------------------------+
| repeat_region | region of genome containing repeating units          |
+---------------+------------------------------------------------------+
| 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     |
+---------------+------------------------------------------------------+
| tr            | transit peptide coding sequence; coding sequence for |
| ansit_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

APPENDIX F\
AMINO ACID SEQUENCE FEATURES

Table F-1 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___Toc53473324 .anchor}Table F‑7: 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 G\
DATA TABLES FOR MOD_RES SEQUENCE FEATURES

Appendix G 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 G-1) and second **Add the following MOD-RES to the
Other Information field** for MOD_RES (Table G-2) 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___Toc53473325 .anchor}Table G‑8: 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___Toc53473326 .anchor}Table G‑9: 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

APPENDIX H\
ADDITIONAL LIPID SEQUENCE FEATURES

Table H-1 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___Toc53473327 .anchor}Table H‑10: 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

APPENDIX I\
ACCEPTABLE CHARACTERS IN THE SEQUENCE DESCRIPTION FIELD

Table I-1 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___Toc53473328 .anchor}Table I‑11: 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

APPENDIX J\
ADDITIONAL MODIFIED_BASE SEQUENCE FEATURES

Table J-1 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___Toc53473329 .anchor}Table J‑12: 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

APPENDIX K\
Technical Notes

[]{#__RefHeading___Toc67224342 .anchor}K.1 Microsoft® Access Notes

PatentIn 3.3 is 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.

K.1.1 Installing Microsoft® Access 97

These general instructions are for Office 97.

1.  Run Setup from the CD.

2.  Select Custom installation. The typical install does not install all
    of the necessary components.

3.  Select Microsoft® Access.

4.  Click on the Change Options button.

5.  Select Advanced Wizards.

6.  Return to main screen.

7.  Select Data Access.

8.  Click on the Change Options button.

9.  Select Database Drivers.

10. Click on the Change Options button.

11. Select dBase & Microsoft® FoxPro Drivers.

12. Return to main screen.

13. Finish installation (or Add).

    K.1.2 Hints and Tips

```{=html}
<!-- -->
```
1.  Patin2xconvert.mdb must be in the same directory as the CWPI.exe and
    must have the help directory in it.

2.  Patin2xconvert.mdb refreshes (updates) its links each time an import
    is done.

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

```{=html}
<!-- -->
```
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).

```{=html}
<!-- -->
```
4.  No relationships are maintained in patin2xconvert.mdb.

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

6.  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.)

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

    []{#__RefHeading___Toc67224343 .anchor}K.2 General Hints and Tips

```{=html}
<!-- -->
```
1.  The installation requires some Dynamic Link Library (DLL)
    registration for each machine.

2.  PatentIn 3.x uses long-names.

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

4.  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.

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

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

7.  Windows 2000/XP defaults to not showing the underlines on the
    toolbar without pressing the Alt-key.

Although no future enhancement releases are envisioned, maintenance
releases may be necessary; however, unreported problems cannot be fixed.
Any future enhancements are expected to exclude the "retail" version of
Windows 95. Windows 95SP2 will still be supported.

[]{#__RefHeading___Toc67224344 .anchor}K.3 installation and testing
notes

With the advent of PatentIn 3.3 new DLLs are installed in the PatentIn
3.3 directory, normally the user\'s personal folder for operating
systems subsequent to Windows XP and C:\\Program Files\\USPTO\\PatentIn
3.3 otherwise.

DDAO35.DLL

MFC42.DLL

MSVCRT.DLL

Each of these are self-registering. As with any new installation it is
recommended that a backup of the system be made first. Should the system
network staff wish to unregister these DLLs because of perceived
conflicts the commands:

regsvr32 --u "C:\\Program Files\\USPTO\\PatentIn 3.3\\ddao35.dll"

regsvr32 --u "C:\\Program Files\\USPTO\\PatentIn 3.3\\mfc42.dll"

regsvr32 --u "C:\\Program Files\\USPTO\\PatentIn 3.3\\msvcrt.dll"

may be executed from Start\|Run. (It is the "--u" that causes these
statements to be unregister statements.) For the user, PatentIn is
designed to be totally uninstalled from the Control Panel Add/Remove
processes.

K.3.1 Testing configurations:

During testing the following configurations were used:

Microsoft® Windows 95

Version 4.00.950 B

Internet Explorer: 3.0(4.70.1158)

Microsoft® Windows 98

Version 4.10.2222 A

Internet Explorer 5.00.2614.3500

Microsoft® Windows NT

Version 4.00,1381

Internet Explorer 5.50.4134.0600

Microsoft® Windows 2000 Professional

Version 5.00.2195

Internet Explorer 5.00.3103.1000

Microsoft® Windows ME

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

Microsoft® Windows XP Professional

Version 2002

Internet Explorer 6.0.2600.0000

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

K.3.2 Internet Explorer Considerations

Internet Explorer ships with several of the DLLs that either Checker
and/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 Microsoft® Windows 98. The user quickly isolated the problem and
informed USPTO that an upgrade to Internet Explorer 5.0 eliminated the
problem.