![](media/image1.emf)

version 2.0

USER MANUAL

# Edition: August 3, 1998

# TABLE OF CONTENTS

1\. Introduction [1](#introduction)

1.1 PatentIn v. 2.0 [1](#patentin-v.-2.0)

2\. System Requirements and Installation
[2](#system-requirements-and-installation)

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

2.2 Pre-Installation Information [2](#pre-installation-information)

2.2.1 Definitions [2](#definitions)

2.2.2 Data Entry Format [3](#data-entry-format)

2.3 Installation [4](#installation)

2.3.1 Internet Download -- INSTALL.EXE (www.uspto.gov)
[4](#internet-download-install.exe-www.uspto.gov)

2.3.2 Floppy Diskette-SETUP.EXE [4](#floppy-diskette-setup.exe)

2.3.3 Installation Procedures [4](#installation-procedures)

2.4 INDEXING DATABASE FILES [5](#indexing-database-files)

2.5 UNINSTALL [5](#uninstall)

2.6 Start the Program [5](#start-the-program)

3\. Structure Organization [6](#structure-organization)

3.1.1 Application Data Entry Screens
[6](#application-data-entry-screens)

3.1.2 Sequence Functions Data Entry Screens
[7](#sequence-functions-data-entry-screens)

3.2 Maneuvering in a Data Entry Screen
[7](#maneuvering-in-a-data-entry-screen)

3.2.1 Data Entry Screen Cursor Control Keys
[7](#data-entry-screen-cursor-control-keys)

3.2.2 Cursor Control Keys for Lists [7](#cursor-control-keys-for-lists)

3.3 PatentIn v. 2.0 Limitations [8](#patentin-v.-2.0-limitations)

4\. Getting Started - Choose An Application
[9](#getting-started---choose-an-application)

4.1 Create [9](#create)

4.2 Open [9](#open)

4.3 Save As [10](#save-as)

4.4 Delete [10](#delete)

4.5 Exit [10](#exit)

5\. The Main Menu and Quick Guide [11](#the-main-menu-and-quick-guide)

5.1 Using the Main Menu [11](#using-the-main-menu)

5.1.1 Applicant Data [11](#applicant-data)

5.1.2 Sequence Functions [11](#sequence-functions)

5.1.3 Exit [12](#exit-1)

5.1.4 Help [12](#help)

5.2 The Quick Guide [12](#the-quick-guide)

5.2.1 OK [12](#ok)

5.2.2 Cancel [12](#cancel)

5.2.3 Exit [12](#exit-2)

5.2.4 Help [12](#help-1)

6\. Tips for Completing Data Entry Screens
[14](#tips-for-completing-data-entry-screens)

6.1 Completing Fields in Data Entry Screens
[14](#completing-fields-in-data-entry-screens)

6.2 Mandatory Fields in Data Entry Screens
[14](#mandatory-fields-in-data-entry-screens)

6.3 Lists With Restricted Vocabulary
[15](#lists-with-restricted-vocabulary)

6.4 Save and Exit Button Behavior Throughout PatentIn Version 2.0
[15](#save-and-exit-button-behavior-throughout-patentin-version-2.0)

7\. Getting Help [16](#getting-help)

7.1 Levels of Help Available [16](#levels-of-help-available)

7.1.1 General Help [16](#general-help)

7.1.2 Field Specific Help [16](#field-specific-help)

7.1.3 Data Entry Screen Help [16](#data-entry-screen-help)

8\. Completing the Application Data
[17](#completing-the-application-data)

8.1 Applicant Information [17](#applicant-information)

8.1.1 Applicant Information Data Entry Screen
[17](#applicant-information-data-entry-screen)

8.1.2 Applicant Information Browse Screen
[18](#applicant-information-browse-screen)

8.2 Current Application Information
[19](#current-application-information)

8.2.1 Current Application Data Entry Screen
[19](#current-application-data-entry-screen)

8.3 Prior Application Information [20](#prior-application-information)

8.3.1 Prior Application Information Data Entry Screen
[20](#prior-application-information-data-entry-screen)

8.3.2 Prior Application Information Browse Screen
[22](#prior-application-information-browse-screen)

9\. Completing the Sequence Functions
[23](#completing-the-sequence-functions)

9.1 Sequence Data Browse Screen [23](#sequence-data-browse-screen)

9.1.1 Organism [24](#organism)

9.1.2 Feature [25](#feature)

9.1.3 Publications [25](#publications)

9.1.4 Author Information Browse Screen
[29](#author-information-browse-screen)

9.1.5 Author Information Data Entry Screen
[30](#author-information-data-entry-screen)

9.1.6 Library of Previously Defined Publications Browse Screen
[30](#library-of-previously-defined-publications-browse-screen)

9.1.7 Import [32](#import)

9.1.8 Modify [33](#modify)

9.1.9 Add [33](#add)

9.1.10 Delete [33](#delete-1)

9.1.11 Restore [33](#restore)

10\. Using the Sequence Editor [34](#using-the-sequence-editor)

10.1 Sequence Editor Screen [34](#sequence-editor-screen)

10.2 Accessing the Sequence Editor [35](#accessing-the-sequence-editor)

10.3 Commands Available from the Menu Bar
[35](#commands-available-from-the-menu-bar)

10.3.1 FILE Menu [35](#file-menu)

10.3.2 Attributes [37](#attributes)

10.3.3 SEARCH Menu [37](#search-menu)

10.4 Exiting [38](#exiting)

10.5 Reordering Sequences [39](#reordering-sequences)

10.6 Code '000' [39](#code-000)

10.6.1 Purpose [39](#purpose)

10.6.2 How to insert the "000" code [40](#how-to-insert-the-000-code)

11\. Completing the Feature Information
[41](#completing-the-feature-information)

11.1 Feature Information Data Entry Screen
[41](#feature-information-data-entry-screen)

11.1.1 Data Entry Block [42](#data-entry-block)

11.1.2 Other Information Window [43](#other-information-window)

11.1.3 Feature Location Window [43](#feature-location-window)

11.2 Choosing a Feature Name/Key [43](#choosing-a-feature-namekey)

11.2.1 Specific Feature Keys [44](#specific-feature-keys)

11.2.2 Additional Information Button
[44](#additional-information-button)

11.3 Specifying the Feature's Location
[44](#specifying-the-features-location)

11.4 Saving the Feature [44](#saving-the-feature)

11.5 Receiving an Error or Warning Message When Saving - The Next Action
to Take
[45](#receiving-an-error-or-warning-message-when-saving---the-next-action-to-take)

11.6 Editing a Feature [45](#editing-a-feature)

11.7 Deleting a Feature [45](#deleting-a-feature)

11.8 Exiting the Feature Information Data Entry Screen
[46](#exiting-the-feature-information-data-entry-screen)

11.9 Annotating a Protein Coding Region
[46](#annotating-a-protein-coding-region)

11.10 Annotating an Internal Stop Codon in a Protein Coding Region
[47](#annotating-an-internal-stop-codon-in-a-protein-coding-region)

11.11 Example of Sequence Annotation
[48](#example-of-sequence-annotation)

12\. Generate an Application Sequence Listing
[50](#generate-an-application-sequence-listing)

12.1 Generating the Sequence Listing
[50](#generating-the-sequence-listing)

12.2 Browse Sequence Listing [50](#browse-sequence-listing)

12.3 Printing the Sequence Listing [51](#printing-the-sequence-listing)

12.4 Editing the Sequence Listing [51](#editing-the-sequence-listing)

12.5 About Sequence Listing Output [52](#about-sequence-listing-output)

12.5.1 Numbering Sequence Listing Residues in the Output
[52](#numbering-sequence-listing-residues-in-the-output)

12.6 Information on How Data is Stored
[53](#information-on-how-data-is-stored)

12.7 Final Steps [53](#final-steps)

13\. Reference [54](#reference)

13.1 Feature Keys - Nucleic Acid [54](#feature-keys---nucleic-acid)

13.2 Feature Keys - Amino Acid [57](#feature-keys---amino-acid)

13.3 Feature Keys - Additional Descriptions
[59](#feature-keys---additional-descriptions)

13.4 List of Numeric Heading Definitions
[60](#list-of-numeric-heading-definitions)

# TABLE OF FIGURES

Figure 3-1: PatentIn v. 2.0 Program Organization
[6](#__RefHeading___Toc424701516)

Figure 4-1: Choose An Application [10](#__RefHeading___Toc424703440)

# 

Figure 5-1: PatentIn v. 2.0 Main Menu/Quick Guide
[13](#__RefHeading___Toc424702696)

# 

Figure 8-1: Applicant Information Data Entry Screen
[18](#__RefHeading___Toc424703405)

Figure 8-2: Applicant Information Browse Screen
[19](#__RefHeading___Toc424703406)

Figure 8-3: Current Application Data Entry Screen
[19](#__RefHeading___Toc424703407)

Figure 8-4: Prior Application Data Entry Screen
[21](#__RefHeading___Toc424703408)

Figure 8-5: Prior Application Information Browse Screen
[22](#__RefHeading___Toc424703409)

# 

Figure 9-1: Sequence Data Browse Screen
[24](#__RefHeading___Toc424703413)

Figure 9 2: Organism Button Options [24](#__RefHeading___Toc424703414)

Figure 9-3: Library of Previously Defined Publication
[26](#__RefHeading___Toc424703415)

Figure 9-4: Bibliographic Information Data Entry Screen
[27](#__RefHeading___Toc424703416)

Figure 9-5: Bibliographic Information, continued Data Entry Screen
[29](#__RefHeading___Toc424703417)

Figure 9-6: Author Information Browse Screen
[30](#__RefHeading___Toc424703418)

Figure 9-7: Import File Manager [32](#__RefHeading___Toc424703419)

# 

Figure 10-1: Sequence Editor [34](#__RefHeading___Toc424703420)

Figure 10-2: Example of 000 Place Holder
[40](#__RefHeading___Toc424703421)

# 

Figure 11-1: Feature Information Data Entry Screen
[42](#__RefHeading___Toc424703425)

#  {#section-5 .unnumbered}

#  {#section-6 .unnumbered}

# 1. Introduction

## 1.1 PatentIn v. 2.0

PatentIn v. 2.0 is a network compatible program designed to expedite the
process of preparing applications containing nucleic acid and
polypeptide sequences. PatentIn v. 2.0 prepares Sequence Listings in
adherence to WIPO ST.25.

PatentIn v. 2.0 solicits all the information needed for a sequence
application, including information about the applicants, prior patent
publications, journal references pertaining to the sequence, and
biological information about the sequence and its source. The program is
accessible in any of four languages: English, German, Spanish, or
French. Wherever possible, PatentIn v. 2.0 allows you to make selections
from pick lists, thus standardizing terminology and reducing typing
errors. You may enter any part of the data at any time and in any order
you wish, and you can easily add, remove, and revise it. You can also
save a partially completed application and finish it during a later
session.

A Sequence Editor is included as part of PatentIn v. 2.0, allowing you
to enter and modify both nucleic acid and protein sequences. Use the
Sequence Editor to enter multiple sequences for each application. You
can import sequence files created by another editor or word processor
(provided they have been stored as ASCII text files) into the PatentIn
v. 2.0 Sequence Editor and incorporate them into your application.

After PatentIn v. 2.0 has collected the data necessary for your
application, it will assist you in creating an Application Sequence
Listing. This is a computer-readable file containing a Sequence Listing
prepared in accordance with WIPO ST.25. You can print a complete copy of
this file and submit it as the paper version of the application.

# 2. System Requirements and Installation

## 2.1 System Requirements

PatentIn v. 2.0 is available for IBM compatible computers using a
Windows ™ operating system. The minimum requirements are as follows:

-   The minimum system hardware requirement is a 386 processor (or
    equivalent) and 4 MB of Random Access Memory (RAM). However, for
    optimum performance, it is recommended that systems have a 486/33mhz
    processor with not less than 8 MB of RAM.

-   The operating system must be Windows 3.1, Windows for Workgroups
    3.11, Windows 95, or Windows NT 3.51 or higher.

-   Operating systems must have a hard disk drive with 20 megabytes free
    disk space plus enough file storage space to accommodate all of the
    sequence files to be imported to the system.

## 2.2 Pre-Installation Information

### 2.2.1 Definitions

Before you begin the installation, you should know some key words and
definitions:

**Application:** This term is used throughout the program and user
manual to denote a discrete Sequence Listing project.

**Cursor:** The marker that indicates where you are on the computer
terminal screen.

**Button:** In a graphics display, a window control that performs a
function when activated with a mouse click or keystroke. (e.g., OK,
Cancel, Exit are typical buttons.)

**Browse (Browser):** A list of items that can be scrolled from top to
bottom with keyboard controls or a mouse. In a graphics display, a
browser is a separate control. (See Listbox)

**Child Window:** In a graphics display, a window within a window.

**Clipboard:** In a Windows™ operating system, an area in computer
memory where data is stored when it either "cut" or "copied." The
contents of the clipboard can be "pasted" (copied to) anywhere in the
operating system. (i.e., a name can be "cut" from the notepad editor and
"pasted" into the name field of PatentIn.). Because all sequences in
PatentIn MUST BE SCREENED, the clipboard CANNOT be used to paste
sequences into the "Sequence Editor."

**Combination Box (or Combobox):** In a graphics display, a control that
is a combination data entry field and list. These controls are
characterized by a down-arrow to the right of the window. When this
arrow is activated with the mouse, the list drops down. This list
behaves like a Listbox (see Listbox, this paragraph.). Once a selection
is made, the list disappears and the selection appears in the data entry
window. In PatentIn Version 2.0, all Comboboxes are "read-only." They
must be filled from the associated lists.

**Control:** In a graphics display, an item that is displayed to perform
a specific function. Buttons perform actions when activated, text boxes
display text, edit boxes accept data entries, listboxes displays lists
of items to browse.

**Data Entry Box (or Window)**: In a graphics display, a control in
which data can be entered by typing or "pasting" from the Windows™
clipboard.

**DOS:** The Disk Operating System.

**Dialog Box**: In a graphics display, a child window within a main
window designed to contain controls (e.g., see buttons, text boxes,
radio menus, window, child window.)

**Directory:** A table of contents for a disk. Separate directories can
be created on your disk drive to store files in an organized manner.

**Listbox**: In a graphic display, a browser control. (See Browse)

**Menu**: A list of actions to be executed when selected and activated.

**Root Directory:** The highest directory level on your hard drive
(usually designated as C:\\ or D:\\) or an external file server on a
network.

**Subdirectory:** A directory within a directory.

**Default:** The option taken if you do not specify a value or make a
decision. The default directory is the directory in which the programs
(including the operating system) look for files, unless you specify
another directory.

**Path:** A combination of the disk drive designation and the directory
name that tells the computer where to look for a file if it is not
contained in the current directory.

**Radio Menu**: In a graphics display, a menu of options that are
connected to operate like the station buttons on a typical radio. In
this application, radio menu selections, once set, are activated with an
**OK** button, which is always the default action if you press
**Enter.**

**Text Box**: In a graphics display, a control to display text.

**Windows™**: A reference to the Microsoft graphical user interface
(GUI) operating system.

**Window**: A rectangle on a video screen to display data. These include
the main window, child window (a window within a window), or a data
entry or display box in a Windows™ based computer application.

### 2.2.2 Data Entry Format

When you type installation commands, you may use upper- or lower-case
letters. If your hard disk drive is not drive C, use the letter of its
designation in place of C for the installation instructions in **Section
2.3** "Installation."

PatentIn v. 2.0 installs the PatentIn v. 2.0 files into a subdirectory
created with that name. Sequence files and the associated Sequence
Listing file are stored in subdirectories of the installation directory
created with the application filename for each new application project.
Since meaningful and systematic names help organize the storage of the
application files on your computer, uniform conventions for file names
are recommended.

PatentIn v. 2.0 stores sequence data in files with the extension .GBS.
PatentIn v. 2.0 also assigns the computer-readable file (the Sequence
Listing) an .APP extension. Since these two file extensions have
specific meanings for PatentIn v. 2.0, they should not be assigned to
any files in your application directory other than application and
sequence files created by PatentIn v. 2.0.

## 2.3 Installation

### 2.3.1 Internet Download -- INSTALL.EXE (www.uspto.gov)

INSTALL.EXE is the PatentIn Version 2.0 single file installation file
that can be downloaded from the Internet. Store this file in any
directory on your PC or a file server. The installation may proceed from
this directory. The INSTALL.EXE file does not need to be in the
destination directory.

### 2.3.2 Floppy Diskette-SETUP.EXE

SETUP.EXE is the PatentIn Version 2.0 two-part file available on two 3½
inch floppy diskettes. Insert disk one into a local floppy drive to
begin installation. The user will be prompted to insert the second disk
midway through the installation.

### 2.3.3 Installation Procedures

[For Windows 3.1]{.underline}, activate the FILE option from the main
window menu bar, then select RUN. Type in the drive and full path name
of the installation file (INSTALL.EXE or SETUP.EXE), or use the browse
button to select the file. Activate OK after the file name is set in the
window. Follow the screen directions. PatentIn creates a group window
and installs the corresponding system icon (BOOKS) in that group window.

[For Windows 95 and Windows NT]{.underline}, use the START button, then
select RUN, then follow installation instructions described above for
Windows 3.1. The PatentIn Version 2.0 icon (BOOKS) is installed in the
Task Bar under Programs.

**NOTE**: **[Mandatory for Windows NT users only]{.underline}:** In
order for the program to run properly, the PatentIn properties **must**
be adjusted to run in separate memory space. After the Windows NT
installation, set the properties of the PatentIn Version 2.0 file to
"Run In Separate Memory Space" by following these directions:

1.  Activate the START button, select "Settings," then select the option
    "Taskbar."

2.  In the Task Bar, select the "Start Menu Properties" folder, then
    click on the "Advanced" button.

3.  Double click on the "Programs" icon, which will display all of the
    program applications under your START menu. Navigate to the PatentIn
    Version 2.0 file, "**right** click" the mouse on the file, then
    select "Properties."

4.  Click into the second tab titled "Shortcut." Click in the box that
    says "Run in Separate Memory Space." Exit by hitting the "OK"
    button.

## 2.4 INDEXING DATABASE FILES

PatentIn Version 2.0 indexes all database files during the installation.
If later, the system experiences an abnormal termination while PatentIn
Version 2.0 is running (e.g., a power failure), the system's databases
may need to be reindexed in order for data to be displayed and printed
accurately.

All users must exit PatentIn before indexing can proceed. After all
users have exited the program, use the File Manager (in Windows 3.1) or
Explorer (in Windows 95 or Windows NT) to activate the file
W_INDEXE.EXE. (For convenience, the corresponding DOS utility, INDEX.EXE
is present as well.) Indexing requires only a few minutes.

## 2.5 UNINSTALL

"Uninstall" utilities are installed in the PatentIn Directory. They
consist of two files that must be run in sequence in order to remove all
subsequently created subdirectories, if application projects have been
added to PatentIn. Use the File Manager (in Windows 3.1) or Explorer in
Windows 95 and Windows NT to activate the file REMOVPRJ.EXE. This file
removes all subdirectories and most of the installation. Then execute
UNWISE.EXE. This will remove the icons from the Windows 95 and Windows
NT installations and the balance of the files. In Windows 3.1, if the
icon and/or group are still on the desktop, delete them by highlighting
and pressing the DELETE key.

## 2.6 Start the Program

5.  Execute the program by doing one of the following.

-   In Windows 3.1, double click on the PatentIn icon.

-   In Windows 95 or NT, click the START button, select the Programs
    directory, click on the PatentIn Version 2.0 icon.

6.  The program will start and prompt you to select a language. Select
    the desired language and click "OK."

7.  Select the "Create" button to enter an application project's
    Filename and File Reference. After "**Save/Exit**," select the
    desired project and click "OK" button.

8.  Follow steps 1 through 3 on the Quick Guide to create a sequence
    listing.

# 3. Structure Organization

PatentIn v. 2.0 contains a series of data entry screens that request
annotated and biological information for the sequence in your patent
application. The Application Data entry screens collect data on the
applicant and the patent application, while Sequence Functions data
entry screens collect data on the nucleic acid or protein sequence.
Access to the Application Data and Sequence Functions data entry screens
is provided through both the *Main Menu* and the menu bar*.*

**Figure 3-1** is a schematic representation of the PatentIn v. 2.0
structure. This diagram illustrates the relationships among the *Main
Menu* items *,* the data entry screens, and the related sub-screens.

![](media/image2.wmf){width="5.998611111111111in"
height="4.315277777777778in"}

[]{#__RefHeading___Toc424701516 .anchor}Figure 3-: PatentIn v. 2.0
Program Organization

### 3.1.1 Application Data Entry Screens

  ----------------------------- -----------------------------------------
  Data Entry Screen Name        Information Recorded

  Applicant                     Applicant's name, address, and related
                                information.

  Current Application           Current application information: Title,
  Information                   Application Number, Filing Date, File
                                Reference

  Prior Application Information Prior patent applications: Application
                                number, Filing date.

  Choose Another Application    Selects a different application, creates
                                a new application, creates a template
                                from an existing application (Save As),
                                or deletes an application.
  ----------------------------- -----------------------------------------

### 3.1.2 Sequence Functions Data Entry Screens

+-----------------------+----------------------------------------------+
| Data Entry Screen     | Information Provided                         |
| Name                  |                                              |
+-----------------------+----------------------------------------------+
| Sequence Data         | Hand key or import sequence data: includes   |
|                       | functionality to Add, Modify, or Delete      |
| Sequence Editor       | sequences                                    |
|                       |                                              |
| Organism Information  | Source of the nucleic acid or protein.       |
|                       |                                              |
| Feature Information   | Areas in the sequence that are biologically  |
|                       | significant.                                 |
| Publication           |                                              |
| Information           | Publications with related sequence           |
|                       | information.                                 |
+-----------------------+----------------------------------------------+
| Generate Sequence     | Create application on disk or paper.         |
| Listing               |                                              |
+-----------------------+----------------------------------------------+
| Browse Sequence       | Browse, print, or copy to disk the sequence  |
| Listing               | listing.                                     |
+-----------------------+----------------------------------------------+
| Help                  | Accesses on-line help.                       |
+-----------------------+----------------------------------------------+

## 3.2 Maneuvering in a Data Entry Screen

### 3.2.1 Data Entry Screen Cursor Control Keys

To move to the next field on a data entry screen, use **Enter** or **↓**
(down arrow key). To go to the previous field on a data entry screen,
use **↑** (up arrow key). Pressing **Enter** while in the last field on
a data entry screen takes you to the first field. Use **←** and **→** to
move to the left or right within a field. Press **Cancel** or **Exit**
to exit the data entry screen and return to the *Main Menu/Quick Guide*.

The following table provides a description of the cursor control keys
and their corresponding functions.

  ----------------------------------------------------- -----------------
  Go to next field on data entry screen.                **Enter** or
                                                        **↓**

  Go to previous field on data entry screen.            **↑**

  Move left within a field.                             **←**

  Move right within a field.                            **→**

  Remove the character to the left of the cursor.       **Bksp**

  Remove the character at the cursor.                   **Del**

  Save data entry screen and return to *Main Menu*      **Cancel** or
                                                        **Exit**
  ----------------------------------------------------- -----------------

### 3.2.2 Cursor Control Keys for Lists

A data entry window with built-in "down arrows" is called a combination
box (or "Combobox"). Comboboxes contain lists. Double clicking on the
down-arrow presents the list. Use ↓ to go to the next item on a list, or
↑ to go to the previous item on a list. In larger lists (such as the
journal names), use the mouse to move within the list. In these large
lists, typing a letter scrolls to the first item beginning with that
letter. On the Organism Name list, which is a 30,000 record indexed
list, scrolling with a mouse is impractical. Therefore, the scroll bar
is disabled and you must either page up/down or begin typing the name of
the organism to search for it.

Use Enter to select the highlighted item on a list. The program will
automatically enter that selection in the appropriate field on the data
entry screen. On lists with OK/Cancel options, select Cancel to exit the
list without making a choice.

The following table provides a description of the cursor control keys
and their corresponding functions.

  ------------------------------------------------------- ---------------
  Go to next item on a list.                              **↓**

  Go to previous item on a list.                          **↑**

  Go to next page of a list.                              **PgDn**

  Go to previous page of a list.                          PgUp

  Move cursor to word that begins with a typed character  A-Z or 0-9
  (on longer lists).                                      

  Select the highlighted item on a list and leave the     **Enter** or
  list.                                                   **OK**

  Leave a list without choosing an item (where            **Exit** or
  applicable).                                            **Cancel**
  ------------------------------------------------------- ---------------

## 3.3 PatentIn v. 2.0 Limitations {#patentin-v.-2.0-limitations .unnumbered}

PatentIn v. 2.0 is designed to be as flexible as possible to allow you
to enter a wide range of data. However, there are limits on the type and
quantity of information PatentIn v. 2.0 can accept.

The limitations existing in PatentIn v. 2.0 are:

-   Each sequence is limited to 50,000 residues in the Sequence Editor.
    If any number of residues exceeds 50,000, whether by hand-keying or
    importing, the editor will truncate the sequence to the first 50,000
    residues.

-   There are no programming limits on the number of sequences that you
    can be added to the sequence list for an application.

-   "Publication Title" and "Invention Title" lengths are limited to 200
    characters each.

-   Feature notes ("Other Information" section) are limited to 200
    characters each, with a maximum of one note per feature.

If these limitations restrict you from entering important information
for your application, you can use a text editor outside PatentIn v. 2.0
to add information to the Sequence Listing. See **Sections 12.3** and
**Section 12.4** for details on editing the Sequence Listing outside
PatentIn v. 2.0 and preparing the printed submission.

# 4. Getting Started - Choose An Application {#getting-started---choose-an-application .unnumbered}

In Windows 3.1 or 3.11, double click on the icon for PatentIn v. 2.0. If
you are using Windows 95 or Windows NT click on the Start button, go to
the programs directory, then click on the PatentIn v. 2.0 subdirectory.

**NOTE**: This section assumes that the program has been installed
according to the instructions found in **Section 2.3** "Installation."

Select your language preference to be used throughout the program. From
the displayed pick list, select from the options: **English, French,
German**, and **Spanish**. The next screen is entitled "**Choose An
Application."** It displays a list of applications plus the following
functional buttons:

## 4.1 Create {#create .unnumbered}

1.  If you would like to create a new application (Sequence Listing),
    click on the **Create** button to create a **New Application.** To
    open an existing application, skip to **4.2 Open**. When creating a
    **New Application,** the program prompts you to enter an application
    name of eight characters or less. [Do NOT use any file name
    extensions!]{.underline} Standard DOS files allow the use of any of
    the following characters:

    **A-Z a-z 0-9 \$ % - @ { } \~ ! \#**

```{=html}
<!-- -->
```
9.  After you type a short name, press **Enter**, then enter a "File
    Reference" name up to 38 characters. If you attempt to exit without
    entering a "File Reference," the program will ask you to input a
    "File Reference" in that field. Entries in both fields and a valid
    file name are required to create a project.

10. When you have finished, click on the Save button. The application
    will be created. Exit will return you to the **Choose An
    Application** screen*.* If you have not saved the application, you
    will be prompted to do so as you exit.

11. Open the application as directed in 4.2 Open.

## 4.2 Open {#open .unnumbered}

If you have already created and saved applications, a list of
applications is displayed in alphabetical order. Navigate through the
application list by using the arrow keys, the PgUp and PgDn keys, or the
mouse to click on the scroll bar. Figure 4-1 shows application list with
one application displayed. You can open the desired application by
highlighting it and pressing **Enter** or the **Open** button, or by
double-clicking on the highlighted file. Proceed to **5.0 Main Menu and
Quick Guide** to complete your application.

## 4.3 Save As {#save-as .unnumbered}

A duplicate of an existing application project can be created as a
template by highlighting an application in the list and clicking on
**Save As.** Enter a new file name and a new file reference name in the
text boxes, **Save**, then **Exit**. All supporting files and records
will be copied from the old application to the newly created
application. The old application will be preserved. If you use a
standard format when preparing applications, it is recommended that you
create a standard application called TEMPLATE with the common fields
completed (i.e. Applicant names, title, etc.). This TEMPLATE application
can be duplicated with the **Save As** button, and will reduce
preparation time.

## 4.4 Delete {#delete .unnumbered}

**Delete** will remove an application from the list, remove all
sequences created, and remove the subdirectory in which they were
stored. Deleted applications cannot be restored. If disk storage is
limited, it may be necessary to delete old applications.

## 4.5 Exit {#exit .unnumbered}

If no application has been opened, **Exit** closes all files and
terminates the program. The system will ask if it is your intention to
exit. If not, the exit procedure is aborted, and control returns to the
**Choose An Application** screen.

If an application is currently open, **Exit** returns to the Main
Menu/Quick Guide, and the current application remains open.

![](media/image3.png){width="5.9375in" height="3.4895833333333335in"}

[]{#__RefHeading___Toc424703440 .anchor}Figure 4-: Choose An Application

# 5. The Main Menu and Quick Guide {#the-main-menu-and-quick-guide .unnumbered}

The *Main* *Menu/Quick Guide* appears after you create or open an
application. (**Figure 5-1** shows the *Main Menu/Quick Guide* screen.)
The *Main Menu/Quick Guide* displays the following information on the
screen:

-   the file name of the current application

-   a *Main Menu* bar displaying the key pull-down menus (*Application
    Data, Sequence Functions, and Help*), and,

-   the *Quick Guide* displays a sequential list of radio buttons that
    guides the user through the steps in creating a Sequence Listing.
    (The same steps are contained in the pull-down menu.)

## 5.1 Using the Main Menu

You select an option by clicking on the menu bar and selecting the
function from the pull-down list. When creating a new application, you
should use the items on the *Main Menu* in the order they are shown.
However, you can complete the data entry screens in any order you
prefer.

After you select an option from the *Main Menu,* the program displays
the corresponding data entry screen with the blank fields to be
completed. Each data entry screen is equipped with field-specific and
general help screens that will assist you with the information to enter
in the field. Instructions are provided on getting a list of the desired
entries. (See **Section 7** "Getting Help" for more information on the
help window.)

The Main Menu options are as follows:

### 5.1.1 Applicant Data

This menu option includes

> **Applicant** (See **8.1** **Applicant Data Information**)
>
> **Current Application** (See **8.2 Current Application Information)**
>
> **Prior Application (**See **8.3 Prior Application Information)**
>
> **Choose Another Application** (See **4.1 Choose and Application**)

### 5.1.2 Sequence Functions

This menu option includes

> **Sequence Data** (See. **9.0** Completing the Sequence Functions)
>
> **Generate Sequence Listing** (See **12.**1 Generating the Sequence
> Listing)
>
> **Browse Sequence Listing** (See **12.2** Browse Sequence Listing)
>
> **Help** -- Help screens from the **Sequence Functions** portion of
> the Help file.

### 5.1.3 Exit

To exit PatentIn v. 2.0, click on the *Exit* at the menu bar, or in the
*Main Menu,* click on the **Exit** button. After you confirm that you
wish to exit PatentIn Version 2.0, the program returns you to Windows.

### 5.1.4 Help

This help button contains keys to the contents of the entire PatentIn
Version 2.0 Help file.

## 5.2 The Quick Guide

Most users will prefer the *Quick Guide*, a menu displayed in the main
window simultaneously with the Main Menu bar. It is organized in
functional groups, in the order in which they are normally executed when
building an application, and with expanded text. (See **Figure 5-1**.)
The *Quick Guide* is more descriptive than the Main Menu. Highlight the
button next to the function to be executed, then click the **OK** button
to activate the function. The *Quick Guide* buttons operate as follows:

### 5.2.1 OK

The **OK** button activates the menu function for the radio button
currently highlighted.

### 5.2.2 Cancel

The **Cancel** button closes the current application and returns to the
**Choose An Application** menu. It functions identically to the
**Application Data/Choose An Application** selection from the Main Menu
bar.

### 5.2.3 Exit

The **Exit** button closes all open files and exits PatentIn Version
2.0. The application asks if this is your intention. If not, the exit
routine is canceled. This button functions identically to the **Exit**
option on the *Main Menu* bar.

### 5.2.4 Help

This is the main **Help** function. It displays the Contents of the
PatentIn Version 2.0 Help file. It calls the same Help screen as does
the **Help** option on the *Main Menu* bar.

[]{#__RefHeading___Toc424702696 .anchor}Figure 5-: PatentIn v. 2.0 Main
Menu/Quick Guide\
![](media/image4.png){width="6.4in" height="5.198611111111111in"}

# 6. Tips for Completing Data Entry Screens

## 6.1 Completing Fields in Data Entry Screens

You can complete most fields by either typing information directly into
the field or selecting from a list of choices.

In most cases, a field that is filled from a list is a Combobox (See
"Combination box" in **2.2.1 Definitions**). Click on the down-arrow to
the right of the combobox to open the list. Click on the selection to
fill the box and hide the list.

Some lists that are very large (e.g. the Organism Name list), or that
are associated with multi-line fields (e.g. the Additional Information
lists) are displayed in a listbox with control buttons and a specialized
search feature.

Data for most functions is collected in one screen. The exception is the
**Publications** data entry function (under the **Sequence Functions**
option of the *Main Menu* or **Enter Sequence Data** option of the
*Quick Guide.)* There are [three]{.underline} Publications related data
entry screens, in addition to associated lists. In these cases, the
buttons **Next** and **Previous** transfer you to separate sub-screens
where you type the information or make selections from lists.

## 6.2 Mandatory Fields in Data Entry Screens

PatentIn v. 2.0 verifies that the following required fields are
completed before compiling the Sequence Listing:

Applicant Information Data Entry Screen

**\<110\>  Applicant Last Name, First Name,** or **Organization Name**

Current Application Information Data Entry Screen

**\<120\>  Invention Title**

**\<130\>  File Reference**

**\<140\>  Application Number (if known)**

**\<141\>  Filing Date (if known)**

Sequence Editor

**\<213\>  Organism**

**\<400\>  Sequence**

Mandatory Information Automatically Supplied by Patentln for Windows

**\<160\>  Number of sequences**

**\<170\>  Software**

**\<210\>  Information for SEQ ID NO**

**\<211\>  Length (of sequences)**

**\<212\>  Type (of sequence: DNA, RNA,** or **PRT)**

## 6.3 Lists With Restricted Vocabulary

PatentIn v. 2.0 provides lists from which you can select values and
options to enter into fields. Some lists are editable, while others are
restricted.

In the Publication Name list in the Bibliographic Information screen, if
the value you want is not on the list, you may type **Other** in the
field. This calls a data entry screen where a journal name can be
entered, which can be added permanently to the journal list for future
reference. While the Organism Name list cannot be edited directly, the
Organism menu has an "**Other**" option, which will permanently add your
new organism name to the list.

The list of feature (Feature Name/Key) is restricted to the values from
tables 5 and 6 in WIPO ST. 25. (See **Chapter 13**.)

## Save and Exit Button Behavior Throughout PatentIn Version 2.0

**Save** and **Exit** button behavior throughout PatentIn is
conventional except for the *Library of Previously Defined Publications*
in **Section 9.1.6**. Any selection made within the *Library of
Previously Defined Publications* will be automatically saved when the
**Exit** button is clicked.

# 7. Getting Help

## 7.1 Levels of Help Available

There are three levels of help available in PatentIn v. 2.0:

-   General help

-   Field specific help for particular fields within a screen

-   Data Entry Screen specific help

### 7.1.1 General Help

General help is obtained by clicking the *Help* option from the *Main
Menu,* from the menu bar, or the Help button on the Quick Guide. The
file displays information about the use of PatentIn v. 2.0 and about
patent-related topics.

Click on the green hypertext to systematically review all help topics.

### 7.1.2 Field Specific Help

Located at the bottom of the screen is the status bar, which provides
context specific instructions based on the placement of the cursor in
any field. To find out what information a field requires, simply move
the mouse indicator over that particular field and the instructions will
appear in the status bar.

### 7.1.3 Data Entry Screen Help

Every data entry screen is also programmed with a Help button. Click on
this button to access context specific help.

# 8. Completing the Application Data

This section describes the functions for completing the Application
Data.

## 8.1 Applicant Information

### 8.1.1 Applicant Information Data Entry Screen

Selecting "Enter Applicant Name(s)" from the *Quick Guide* initially
presents the Applicant Information data entry screen if there are no
applicants. When applicants are present, the "Applicant List" browse
screen is presented, containing a list of all applicants. From this
screen you have the option to Modify, Add, or Delete an applicant
record.

The Applicant data screen that follows is used to enter the names of the
applicants, as well as optional correspondence information for the
application. In the Applicant Information data entry screen, you must
first indicate whether the applicant is an Individual or Organization.
If you select Individual, which is the default option, the Applicant
Information data entry screen then allows you to enter the name(s) (Last
Name, Suffix, First Name, and Middle Initial) of the person(s) applying
for the patent. Choosing Organization allows you to enter the
Organization Name.

"First Name" and "Last Name" for Individual, and "Organization Name" for
Organization are mandatory entries. Correspondingly, the text for these
fields is shown in the color red.

You may also enter optional information in the remaining fields
(Address, City, State, ZIP, Phone Number, Fax Number and E-mail). These
fields are for your internal user records and reference.

When you have finished entering the applicant information, click either
the Save or Exit buttons. If you click on the Save button, the
information entered is saved to the current application. If you click on
the **Exit** button without saving, the program will prompt you to save
the entered information. If you elect not to save your data and there
are no applicants, you will be returned to the *Main Menu*/*Quick
Guide*. If there are any applicants, you are returned to the *Applicant
List* browse screen. Exiting the *Applicant List* returns you to the
*Main Menu/Quick Guide.* **Figure 8-1** shows an example of the
\"Applicant Data\" data entry screen.

![](media/image5.png){width="6.0in" height="4.125in"}

[]{#__RefHeading___Toc424703405 .anchor}Figure 8-: Applicant Information
Data Entry Screen

### 8.1.2 Applicant Information Browse Screen

After saving the information in the Applicant Data Entry Screen, you
automatically access the Applicant Information browse screen. **Figure
8-2** shows an example of the *Applicant List* browse screen. This
browse screen is a list of all applicants entered for the current
application. While in this browse screen, your options are:

-   **Modify** -You may edit the information on a particular applicant
    by highlighting the desired applicant and clicking on the **Modify**
    button.

-   **Add** -- You may add more applicants to the application by
    clicking the **Add** button and entering the appropriate
    information.

-   **Delete** -- You may delete an applicant by highlighting the
    particular applicant and clicking the **Delete** button.

-   **Exit** -- After entering all applicants, press the **Exit** button
    from the browse screen to return to the *Main Menu/Quick Guide*.

    ![](media/image6.png){width="5.8125in"
    height="2.3020833333333335in"}

[]{#__RefHeading___Toc424703406 .anchor}Figure 8-: Applicant Information
Browse Screen

## 8.2 Current Application Information {#current-application-information .unnumbered}

### 8.2.1 Current Application Data Entry Screen

Selecting "Enter Current Application Information" from the *Quick Guide*
presents the Current Application data entry screen*.* This screen
collects information about the application that is currently being
filed. The fields in this screen are: **Title, Application Number,
Filing Date,** and **File Reference.** These fields collect required
information about the current application. Figure 8-3 shows an example
of the Current Application Data Entry Screen.

**NOTE**: If you submit the Sequence Listing after filing the original
application, such as an amendment, you must provide the **Application
Number** and **Filing Date.**

![](media/image7.png){width="5.15in" height="3.1597222222222223in"}

[]{#__RefHeading___Toc424703407 .anchor}Figure 8-: Current Application
Data Entry Screen

#### 8.2.1.1 Title

Enter a title for the application in this field. This is a mandatory
field.

A 200-character field is displayed for entering, reviewing, and editing
the title. To leave the title field, press the **Tab** key, and the
cursor will move to the next field.

#### 8.2.1.2 Application Number

If known, enter the application number in the format that is required
for the receiving office you are submitting your sequence listing to. If
you are unsure of the required format for this field, refer to WIPO
ST.10/C for the proper format to use. PatentIn will *not* check the
Application number field for correct format.

**NOTE**: The Application Number field is not mandatory, but if
completed, you must complete both the Application Number and Filing Date
fields.

For PCT applications, type the complete PCT application number including
the letters PCT, a slash, a two-letter code indicating the Receiving
Office, a two-digit indication of the year, a slash, and a five-digit
number in the Application Number field; for example, PCT/US88**/99999**.

#### 8.2.1.3 Filing Date

Enter the original filing date of the application in this field, if
known. Enter the date in the format **YYYY-MM-**DD, for example,
1997-12-31.

**NOTE**: The Application Number field is not mandatory, but if
completed, you [must complete]{.underline} both the **Application
Number** and **Filing Date** fields.

#### 8.2.1.4 File Reference

This is a description of the application used as a file reference. It
may be a maximum of 38 characters and spaces. The data that was entered
in the "File Reference" field when you created your project will be
shown here. The file reference name can be edited at any time by using
this screen.

When you have finished entering the application information, click
either the Save or Exit buttons. If you click on the Save button, the
information entered is saved to the current application. If you click on
the **Exit** button, the program will prompt you to save the entered
information, then returns you to the *Main Menu/Quick Guide*.

## 8.3 Prior Application Information {#prior-application-information .unnumbered}

### 8.3.1 Prior Application Information Data Entry Screen

Selecting "Enter Prior Application Information" from the *Main Menu* for
the first time, displays the Prior Application Information data entry
screen. This screen collects information about any previous domestic,
foreign priority, or international patent applications pertaining to the
sequence currently being patented.

If any records are present, the first screen will be a list of these
records. From this list you may Modify, Add, or Delete a Prior
Application record.

The fields to be completed in this screen are the Application Number and
Filing Date. **Figure 8-4** shows an example of a Prior Application
Information Data Entry Screen.

**NOTE**: The Prior Application data entry screen is not mandatory, but
if filled out, both the Filing Date and Application Number fields
[must]{.underline} be completed.

![](media/image8.png){width="5.416666666666667in" height="2.65625in"}

[]{#__RefHeading___Toc424703408 .anchor}Figure 8-: Prior Application
Data Entry Screen

#### 8.3.1.1 Application Number

If known, enter the application number in the format that is required by
the receiving office to which you are submitting your sequence listing.
If you are unsure of the required format for this field, refer to WIPO
ST.10/C for the proper format to use. PatentIn will not check the
Application number field for correct format.

**NOTE:** The Application Number field is not mandatory, but if
completed, you must complete both the Application Number and Filing Date
fields.

If you are entering a PCT application, type the complete PCT application
number, including the letters **PCT**, a slash (/), a two-letter code
indicating the Receiving Office, a two-digit indication of the year, a
slash, and a five-digit number in the **Application Number** field; for
example, **PCT/US88/99999**.

#### 8.3.1.2 Filing Date

Enter the date on which the prior application was filed. Enter the
Filing Date in the format YYYY-MM-DD, for example, 1997-12-31.

**NOTE:** The Application Number field is not mandatory, but if
completed, you must complete both the Application Number and Filing Date
fields.

When you have finished entering the applicant information, click either
the Save or Exit buttons. If you click on the Save button, the
information entered is saved to the current application. If you click on
the **Exit** button, the program will prompt you to save the entered
information, then opens the Prior Application browse screen if there are
any Prior Application records. Otherwise, PatentIn returns to the *Quick
Guide*.

### 8.3.2 Prior Application Information Browse Screen

After saving the information entered in the Prior Application data entry
screen, you are returned to the Prior Application Information browse
screen which displays a list of all prior applications relevant for the
current application. **Figure 8-5** shows an example of the Prior
Application Information Browse Screen. While in this browse screen, you
have the following options:

-   **Modify** --You may edit the information on a particular prior
    application by highlighting the desired applicant and clicking on
    the **Modify** button.

-   **Add** -- You may add prior applications to the current application
    by clicking the **Add** button and entering the appropriate
    information.

-   **Delete** -- You may delete a prior application by highlighting the
    particular applicant and clicking the **Delete** button.

-   **Exit** -- After entering all of the applicants, press the **Exit**
    button from the browse screen to return to the *Main Menu/Quick
    Guide*.

![](media/image9.png){width="5.166666666666667in"
height="2.3854166666666665in"}

[]{#__RefHeading___Toc424703409 .anchor}Figure 8-: Prior Application
Information Browse Screen

# 9. Completing the Sequence Functions

The *Sequence Functions* menu options enable you to enter data relevant
to your application. Selecting "Enter Sequence Data" from the Quick
Guide accesses the Sequence Data browse screen. From this screen,
entitled "Sequence Functions for Current Highlighted Sequence," you may
access the supporting functions for these sequences.

These supporting functions include buttons to open the other data entry
screens for Organism, Feature, and Publications. They also include
buttons to **Modify** a sequence on the list, **Add** a new sequence in
the Sequence Editor, **Import** a sequence to the list from another
directory, **Delete** a sequence from the list, or **Restore** a
previously deleted sequence to the list.

## 9.1 Sequence Data Browse Screen

Select "Enter Sequence Data" from the *Quick Guide* to access the
Sequence Data browse screen. **Figure 9-1** shows an example of the
Sequence Data Browse Screen. The Sequence Data browse screen lists the
file name, type, and length of sequence, current numerical order of
sequences, and whether an Organism -- a mandatory field -- has been
assigned to the sequence.

The order of sequences may be changed at any time by "drop and drag."
(For more information, see **Section 10.4** "Reordering Sequences.") The
order of sequences is renumbered automatically, and therefore always
appears in ascending order. The order number may not be consecutive if
there are deleted sequences, since deleted sequences retain their order
number.

The order numbers correspond to the order in which the sequences are
evaluated when compiling the sequence listing. However, this may not
necessarily be the sequence number itself, since sequence numbers are
assigned at the time the sequence is compiled based on visible sequences
only. Furthermore, CDS features insert additional sequences with their
own sequence numbers. (See **Section 11.9** "Annotating a Protein Coding
Region" for additional information.)

This screen also provides important links to other screens, such as
**Organism Information, Feature Information, Publications Selections
Browse Screen,** **Import, Restore,** and the **Sequence Editor**. These
screens, with the exception of the Sequence Editor and Feature
Information, are discussed in the following sections.

**NOTE:** For details on the Sequence Editor, refer to **Section 10**
"Using the Sequence Editor." For details on the Feature Information,
refer to **Section 11** "Completing the Feature Information."

![](media/image10.png){width="5.822916666666667in"
height="3.0833333333333335in"}

[]{#__RefHeading___Toc424703413 .anchor}Figure 9-: Sequence Data Browse
Screen

### 9.1.1 Organism

To assign an organism to a sequence, first highlight the desired
sequence, then click on the **Organism** button from the Sequence Data
browse screen to access an intermediate screen. In accordance with WIPO
ST.25, each sequence must specify the original source organism. This
screen displays a list box enabling you to select from the radio-button
options of **Organism, Unknown, Other,** and **Artificial Sequence.
Figure 9-2** shows an example of the Organism Button selections.

> ![](media/image11.png){width="6.145833333333333in" height="3.28125in"}

[]{#__RefHeading___Toc424703414 .anchor}Figure 9-: Organism Button
Options

**Select Organism Name** opens a list of selected known Organism names.
You locate your selections by typing the organism name in the text box
below the list or by using the cursor control keys: page down/up or
arrow down/up. Do not mouse-click in the text box first. Just
immediately start typing the first characters of the organism name. If
your desired organism name is not in the list, click on cancel and
select "Other" within the main organism menu.

If you select **Unknown**, you will also be presented with a data entry
box to describe the Unknown organism further. This entry is mandatory as
per WIPO ST. 25. It appears as a Feature note associated with this
sequence, and can be further modified in the Feature section.

Select the **Other** radio button if the organism you require is not
indicated on the "Select Organism Name list." A dialog box will open,
allowing you to enter the appropriate scientific name of the organism.
WIPO ST.25 dictates that the response for the organism field be the
Latin species name. The user will be asked to type in the name twice if
the new name will be permanently added to the "Organism" list.

If you select **Artificial Sequence**, you will also be presented a data
entry box to describe the Artificial Sequence further. This entry is
mandatory. It appears as a Feature note associated with this sequence,
and can be further modified in the Feature section.

### 9.1.2 Feature 

Click on the **Feature** button to access the Feature Information data
entry screen. (For detailed information about this screen, refer to
**Section 11** "Completing the Feature Information.")

### 9.1.3 Publications 

PatentIn v. 2.0 allows you to enter as many references relating to your
sequence as needed. These publications are entered on the Bibliographic
Information data entry screens and author screens, which are entered
through the *Library of Previously Defined Publications* Bibliographic
Information Data Entry Screen (See **Figure 9-3**).

> ![](media/image12.png){width="5.864583333333333in"
> height="4.072916666666667in"}

[]{#__RefHeading___Toc424703415 .anchor}Figure 9-: Library of Previously
Defined Publication

Activate **Add** to open the first Bibliographic Information data entry
screen. Once you have completed the screen's fields, click on the
**Next** button to access additional fields and screens. The third
screen is a list of **Authors**, from which individual author records
may be selected to **Modify**, or a blank screen opened to **Add**
authors.

Each field on the Bibliographic Information data entry screen is
described in the following sections. **Figure 9-4** shows an example of
the Bibliographic Information Data Entry Screen.

![](media/image13.png){width="5.395833333333333in"
height="3.5416666666666665in"}

[]{#__RefHeading___Toc424703416 .anchor}Figure 9-: Bibliographic
Information Data Entry Screen

#### 9.1.3.1 Publication Type

For this field, you must select one of the following publication types
from a list: **Journal, Patent,** or **Thesis.** Clicking on the field
enables you to select your entry choice.

+--------------------+-------------------------------------------------+
| Publication Type   | Description                                     |
+--------------------+-------------------------------------------------+
| Journal            | Journal publication. The Journal category       |
|                    | includes journals (such as *Cell* or *Gene*) as |
|                    | well as serial publications (such as *Cold      |
|                    | Spring Harbor Symposia* volumes and *Methods in |
|                    | Enzymology).* A list of approximately 300       |
|                    | journals is available under the "Journal Name"  |
|                    | option, and the "Other" selection permits       |
|                    | adding another. This field also permits         |
|                    | entering a database accession number and        |
|                    | database entry date.                            |
|                    |                                                 |
|                    | ***NOTE**: If the sequence will eventually      |
|                    | appear in a journal yet to be published, choose |
|                    | Journal. You can then indicate the sequence\'s  |
|                    | pre-publication state in the next field.*       |
+--------------------+-------------------------------------------------+
| Patent/Published   | Patent/Application publication. This selection  |
| Application        | changes the fields in the first Bibliographic   |
|                    | Information screen to the Publication Database  |
|                    | Entries screen. Journal information is removed  |
|                    | and a pop-up data entry box is presented to     |
|                    | enter a published application's number, filing  |
|                    | date, and publication date.                     |
+--------------------+-------------------------------------------------+
| Thesis             | Thesis publication. This selection presents the |
|                    | same data entry fields as Journal, except the   |
|                    | database accession number, database entry date, |
|                    | and page number references are omitted.         |
+--------------------+-------------------------------------------------+

#### 9.1.3.2 Publication Name

If the specified sequence appears in a journal, click in the Publication
Name field and select the appropriate journal name from the pick list of
approximately 300 journals. This list is alphabetically indexed. To find
the associated journal, click in the field to display a scrolling list
of the journals from which to make your selection. A journal can also be
located by first-letter keystroke (i.e., pressing the letter "U" calls
the first journal beginning with "U." Pressing "U" again skips to the
next item beginning with "U." etc.).

After you make a selection, the journal name appears in the field. If
the journal is not on the list, select "Other" from the list in order to
access a data entry dialog box. In this box, type the name or official
abbreviation of the journal that will appear in the Publication Name
field. The name needs to be typed in twice to ensure spelling if it will
be permanently added to the Journal list.

#### 9.1.3.3 Publication Date

Enter the year or the season in which the article, journal, serial, or
thesis was published in the **Publication Date** field. If this
information is unknown, skip this field. This is NOT a standard date
field and does not need to be completed in the conventional date format.

#### 9.1.3.4 Volume and Issue

Enter the volume of the journal or serial in the **Volume** field. If
the Publication Information includes an issue number, enter it in the
**Issue** field.

#### 9.1.3.5 Start Page and End Page

In the appropriate field, enter the page on which the Publication
Information starts and ends. In the **End Page** field, include the
pages containing references. You do not need to enter page numbers for a
thesis, and therefore these fields are not visible.

**NOTE:** At this point in the screen, you will need to click on the
**Next** button to access the remaining fields. See **Figure 9-5** for
an example of the Bibliographic Information Data Entry Screen,
continued.

#### 9.1.3.6 Title

This field should contain one of the following: Journal Article Title,
Serial Article Title, or Thesis Title.

Because the Publication Title is a lengthy field, PatentIn v. 2.0
provides a simple mini-editor for entering, reviewing, and editing. The
entered text is considered a single "line," and the editor automatically
wraps and displays it, up to 4 lines at a time, on the screen. The
**Title** field is limited to 200 characters of text. When you are
finished typing, press either the **Tab** or **Enter** key to move to
the next field.

#### 9.1.3.7 Relevant Residues (From/To Fields)

These fields indicate the part of the sequence, or "residues," reported
in a particular publication. In many cases, the entire sequence is
included in a publication; however, in other cases, only a portion of
the sequence is included in a publication. In the **From** field, enter
the first residue of your application sequence reported in the
publication you are entering. In the To field, enter the last residue of
your application sequence reported in this publication.

If the numbering scheme used for the residues in the publication differs
from that used by PatentIn v. 2.0, the values that you entered in the
**From** and **To** fields should reflect the numbering as it appears in
the PatentIn v. 2.0 Sequence Editor*.* The PatentIn v. 2.0 Sequence
Editor always begins numbering at \"**1**\" and rejects negative
numbers.

> ![](media/image14.png){width="5.322916666666667in"
> height="3.2604166666666665in"}

[]{#__RefHeading___Toc424703417 .anchor}Figure 9-: Bibliographic
Information, continued Data Entry Screen

### 9.1.4 Author Information Browse Screen

Clicking on the Next button accesses the Author Information browse
screen. Figure 9-6 shows an example of the Author Information Browse
Screen. The authors of the publication are displayed in a list. Unlike
comparable lists in PatentIn, this list appears whether or not authors
are present. The options in this screen are:

-   **Modify** -You may edit the information on a particular author by
    highlighting the desired author name and clicking on the **Modify**
    button.

-   **Add** -- You may add more authors to the application by clicking
    the **Add** button and entering the appropriate information.

-   **Delete** -- You may delete an author by highlighting the
    particular author name and clicking the **Delete** button.

-   **Exit** -- After entering all authors, press the **Exit** button
    from the browse screen to return the "Library of Previously Defined
    publications."

    ![](media/image15.png){width="6.5125in"
    height="2.8069444444444445in"}

[]{#__RefHeading___Toc424703418 .anchor}Figure 9-: Author Information
Browse Screen

### 9.1.5 Author Information Data Entry Screen

If you select **Modify** or **Add** from the Author Information browse
screen, you access the Author Information data entry screen. In this
screen, enter the names of the authors of the Bibliographic Information
in the order in which they appeared (or will appear) in the publication.

When you have finished entering the author information, click either the
Save or Exit buttons. If you click on the **Save** button, the
information entered is saved to the current application. If you click on
the **Exit** button, the program will prompt you to save the entered
information, then returns you to the Bibliographic Information browse
screen.

### 9.1.6 Library of Previously Defined Publications Browse Screen 

Click on the **Publications** button to access the *Library of
Previously Defined Publications* browse screen, if any are present. This
screen lists all publications with information relating to the current
application that have been created, and permits selected publications to
be applied to the current sequence (identified in the title bar). This
is done by double-clicking on the record, which toggles the left column
in the record with an "X" or a blank to mark and unmark the record. A
check box and radio menu options are presented below the function
buttons to apply these selections to other sequences as well.

This screen serves as a master list of all references for the entire
sequence listing and the individual selections for the current sequence
under consideration, and provides tools to expedite the process of
selecting publications. Figure **9-3** shows an example of a *Library of
Previously Defined Publications* browse screen.

After saving all the information entered in the Author Information data
entry screen and browse screen, you are returned to the initial library
browse screen that lists all publications and publication types entered.
**Figure 9-3** shows an example of the Library of Previously Defined
Publications. While in this browse screen your options are:

-   **Modify** --You may edit the information on a particular
    publication by highlighting the desired applicant and clicking on
    the Modify button.

-   **Add** -- You may add more publications to the application by
    clicking the Add button and entering the appropriate information.

-   **Delete** -- You may delete a publication by highlighting the
    particular applicant and clicking the Delete button.

-   **Restore** -- You may undo all previous deletions in this screen.

-   **Exit** -- After entering all publications, press the Exit button
    from the browse screen to save data and return to the Main
    Menu/Quick Guide.

To apply the selections to other sequences mark the check-box that
states, "Check here to apply selection to more than one sequence upon
exiting." That enables the radio menu of the following choices:

-   **All Sequences --** All sequences current in the list will reflect
    the same publications selections. However, sequences that are
    subsequently added will not be effected.

-   **Remaining Sequences --** All sequences after the current sequence
    in the sequence list will reflect the same publications information.
    Each sequence will retain its publications selection even if the
    order is subsequently changed.

-   **Range of Sequences** -- A specific range of sequences can be
    specified, based on the current order. There are positions to enter
    the starting **(From)** and ending (**To**) sequence order numbers.
    Each sequence will retain its publications selection even if the
    order is subsequently changed.

The selections are applied when the screen is exited. (See Figure
**9-3**.)

### 9.1.7 Import 

Click on the **Import** button to import ASCII sequence files located on
a diskette, hard drive, or file server. Each imported sequence must be
within a separate file. However, PatentIn can "bulk" import if the user
selects multiple files. The file size is displayed with the file name in
the Files window to facilitate identifying files to import. Figure 9.7
shows an example of the Import File Manager. PatentIn can import any
[text]{.underline} file. Word processing and database files cannot be
read unless first stored as text files.

![](media/image16.png){width="6.083333333333333in"
height="3.2291666666666665in"}

[]{#__RefHeading___Toc424703419 .anchor}Figure 9-: Import File Manager

**Import** has five filters to select from: **DNA Filter**, **RNA
Filter**, **Combined DNA/RNA, PRT One Letter Filter**, and **PRT Three
Letter Filter**. When you open a non-PatentIn v. 2.0 file, the program
removes all characters except valid sequence characters. PatentIn v. 2.0
also removes all invalid characters such as line breaks, spaces, and
numbers, etc. when opening the sequence, and saves the sequence in
PatentIn v. 2.0 format with a .GBS extension. The following characters
remain in the sequence after filtering (characters may be in either
upper or lowercase):

  --------------------------- -------------------------------------------
  **DNA Filter**              a, g, c, t, y, r, m, k, s, w, h, b, v, d, n

  **RNA Filter**              a, g, c, u, y, r, m, k, s, w, h, b, v, d, n

  **Combined DNA/RNA Filter** a, g, c, u, r, y, m, k, s, w, b, d, h, v,
                              n, t

  **PRT One Letter Protein    A, B, C, D, E, F, G, H, I, K, L, M, N, P,
  Filter**                    Q, R, S, T, V, W, X, Y, Z

  **PRT Three Letter Protein  Refer to **Section 10.3.3.5** "Amino Acid
  Filter**                    Codes Table"
  --------------------------- -------------------------------------------

**NOTE:** The **RNA** and **DNA Filters** do not perform any conversions
when you import the sequence. For example, if you select the RNA Filter
and there are T\'s in the sequence, they will be filtered out, not
converted to U\'s. The **PRT One-Letter Filter** will also remove all
characters that are not standard one-letter amino acid characters (see
**Sections** **9.3.3.4** and **9.3.3.5**). **PRT Three-Letter Filter**
will read valid three-letter amino acid groups and convert them to **PRT
One Letter format**. Three-letter groups can be in upper or lower case,
and may be separated by a space character. When the Sequence Listing is
printed, amino acid residues will be shown in the required three-letter
format.

You can import sequence files that have been created with other editors,
word processing programs or data analysis programs provided they have
been stored as text files. For sequences that will be imported into
PatentIn v. 2.0, be sure to specify a text mode when you save a sequence
file from a word processor.

### 9.1.8 Modify

The **Modify** button opens a previously entered sequence into the
Sequence Editor. Highlight the desired sequence and activate the button,
double click on the sequence record, or press **Enter.** See **Chapter
10** for detailed instruction on using the Sequence Editor.

### 9.1.9 Add

The **Add** button opens the Sequence Editor to create a new sequence
(by hand-keying). The new sequence is not saved to the project file
until saved within the Sequence Editor. See **Chapter 10** for detailed
instruction on using the Sequence Editor.

### 9.1.10 Delete

A sequence record may be deleted by highlighting the target file and
activating **Delete.** This hides the sequence and the associated
**Organism**, **Feature**, and **Publications** selections. These files
remain resident within PatentIn v. 2.0 and may be recalled. See
**Section 9.1.11** "Restore" on procedures to recall a deleted sequence.
The sequence files are destroyed only when an Application Project is
deleted from the *Choose An Application* screen.

### 9.1.11 Restore

A deleted sequence may be restored using the **Restore** button. When
the button is activated, it presents a list of all sequence files that
have been deleted for this Application Project. Highlight the sequence
to restore and select *OK.* Only one sequence can be restored at a time.
The new sequence is restored in the same position that it was in before
being deleted, along with all of its associated **Organism**,
**Feature**, and **Publications** selections.

# 10. Using the Sequence Editor {#using-the-sequence-editor .unnumbered}

## 10.1 Sequence Editor Screen {#sequence-editor-screen .unnumbered}

The Sequence Entry Window displays bases of nucleic acid or residues of
protein sequence entries. The design of the Sequence Editor is different
from the Application data entry screens. The Sequence Editor screen is
divided into two parts: a **Menu Bar** including a *Help* option at the
top, and a **Sequence Entry Window** encompassing most of the screen.
The menu bar provides access to three menus: **File, Attributes, and
Search,** which are described in **Section 10.3** "Commands Available
from the Menu Bar."

There are two ways to enter a sequence: type the sequence directly into
the Sequence Entry Window, or open a sequence from another file into the
editor. Opening files into the editor is described in the File Menu
section below under the **Open** option (see **Section 10.3.1.2**
"Open").

Additionally, the Sequence Entry Window displays residues in groups of
ten, with sixty residues on each line. The rightmost column of the
window displays the number of the last residue on that line. The
sequence length and cursor positions are displayed at the bottom of the
Sequence Editor screen. **Figure 10-1** shows an example of the Sequence
Editor screen.

![](media/image17.png){width="6.5125in" height="3.95in"}

[]{#__RefHeading___Toc424703420 .anchor}Figure 10-: Sequence Editor

## 10.2 Accessing the Sequence Editor {#accessing-the-sequence-editor .unnumbered}

To edit a sequence in the Sequence List in the Sequence Data browse
screen, highlight the sequence and click on the **Modify** button**,**
or double click on the desired sequence. This will open that sequence
within the Sequence Editor.

To create a new sequence, activate the **Add** button. A radio menu will
ask for the Sequence Type (the default is **DNA).** After designating
the sequence type, the *Sequence Editor* will open with the appropriate
filter key set for the operator to type in a new sequence.

At the top of the Sequence Editor is the menu bar with the options
**File**, **Attributes**, and **Search**. Click on any of the options on
the Menu Bar to activate that particular option. Press **Cancel** to
leave the option that you just chose from the Menu Bar.

## 10.3 Commands Available from the Menu Bar {#commands-available-from-the-menu-bar .unnumbered}

The following sections explain the functions of the Sequence Editor menu
bar and the different options available.

### 10.3.1 FILE Menu

The commands in this menu perform various file-related functions, or
allow you to exit the Sequence Editor*.* The commands in this menu are
**New, Open**, **Save**, **Save As**, and **Cancel**. Each command is
discussed below.

#### 10.3.1.1 New

**New** allows you to create a new sequence.

#### 10.3.1.2 Open

Use the **Open** command to open existing sequence files into the editor
to build a new sequence file. The sequences must be in text only (or
ASCII) format. In addition, each sequence file should contain only one
sequence; the **Open** command cannot separate multiple sequences
contained in one file. However, PatentIn v. 2.0 can import both PatentIn
and non-PatentIn formatted text files. Any invalid characters in the
imported text file will be filtered out.

**Open** has five filters to select from: **DNA Filter**, **RNA
Filter**, **Combined DNA/RNA, PRT One-Letter Filter,** and **PRT
Three-Letter Filter**. When you open a non-PatentIn v. 2.0 file, the
program removes all characters except valid sequence characters.
PatentIn v. 2.0 also removes all invalid characters such as line breaks,
spaces, and numbers, etc. when opening the sequence. The sequence
becomes part of whatever sequence is in the editor. The following
characters remain in the sequence after filtering (characters may be in
either upper or lowercase, depending on sequence type):

  ----------------------- -----------------------------------------------
  **DNA Filter**          a, g, c, t, y, r, m, k, s, w, h, b, v, d, n

  **RNA Filter**          a, g, c, u, y, r, m, k, s, w, h, b, v, d, n

  **Combined DNA/RNA      a, g, c, u, r, y, m, k, s, w, b, d, h, v, n, t
  Filter**                

  **PRT Filter**          A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R,
                          S, T, V, W, X, Y, Z
  ----------------------- -----------------------------------------------

**NOTE:** The **RNA** and **DNA Filters** do not perform any conversions
when you import the sequence. For example, if you select the RNA Filter
and there are T\'s in the sequence, they will be filtered out, not
converted to U\'s. The **PRT One-Letter Filter** will also remove all
characters that are not standard one-letter amino acid characters (see
**Sections** **10.3.3.** and **10.3.3.5**). The **PRT Three-Letter
Filter** will convert any valid three letter grouping into its one
letter counterpart as it is brought into the editor.

**WARNING:** If the sequence characters shown in the previous table
appear anywhere in the file except the sequence, you must use a text
editor outside PatentIn v. 2.0 to delete them before importing the
sequence. Otherwise, PatentIn will import the character as a codon. Be
sure to check that the length of the imported sequence is as expected.
The maximum length of any sequence file can be only 50,000 characters.
The source file may be any length so long as the number of valid codons
does not exceed 50,000.

To open a sequence into the Sequence Editor, click on Open. You will
access the import file manager, in which you indicate the drive,
directory, and file name of the sequence you wish to open. You will be
prompted to open the file into the editor in one of three ways: Append
the upcoming sequence to the currently displayed sequence, Insert the
sequence at the cursor, or Replace the current sequence entirely.

After importing the sequence, click either the **Save** or **Exit**
button. You are prompted to save the file under the current sequence
name, the imported file name, or to display without saving. Once you
make the save decision, you are prompted to import another sequence or
return to the Sequence Editor.

#### 10.3.1.3 Save

Use **Save** to save a copy of the sequence in a file on your hard
drive.

All sequences introduced via the Open button become part of the current
sequence. If the current sequence does not have a file name (i.e., it is
a new sequence) you will be prompted to give that file a name upon
activating the Save or Exit buttons. Otherwise, the contents of the
editor will be saved to the current file without prompting.

**CAUTION**: The Sequence Editor is always in the Read/Write mode. [Any
keystrokes may alter the sequence!]{.underline}

#### 10.3.1.4 Save As

**Save As** allows you to save the contents of the Sequence Window with
a different name. You can then use the file in a different application
or for another purpose. When you select the **Save As** command, the
program prompts you to enter the new file name you would like to give
the sequence. PatentIn v. 2.0 automatically adds the .GBS file
extension. If you type the name of a file that already exists, the
program prompts you to change the name of the new file.

#### 10.3.1.5 Cancel

**Cancel** allows you to close the **FILE menu** options.

### 10.3.2 Attributes

The **Attributes** button calls the same sequence modification buttons
as found on the Sequence Data browse screen and described in the
paragraphs: **9.1.1 Organism, 9.1.2 Feature,** and **9.1.3**
**Publications**.

### 10.3.3 SEARCH Menu

The commands in this menu allow you to locate a specific series of
residues within your sequence. The menu options are **Find, Next,** and
**Cancel.**

#### 10.3.3.1 Find

The **Find** option opens a dialog box in which you enter the residue to
find. The residue you want to find is called a **Search String**.
**Find** command searches the sequence from the first position forward
to the first occurrence of the Search String. You may type up to 10
characters.

Click OK once you have finished typing the characters. PatentIn v. 2.0
searches through the sequence looking for the characters you typed,
ignoring spaces or line breaks. If the program finds the series, the
cursor moves to the first residue of the series. If the program does not
find the series, the cursor remains where it was before you selected the
**Find** command and a message reports that the string was not found.

#### 10.3.3.2 Next

The **Next** option command searches for subsequent occurrences of the
set of residues you found last. Using **Next** eliminates the need to
re-type the set of residues each time you want to find them.

#### 10.3.3.3 Cancel

**Cancel** allows you to close the **SEARCH menu** options.

#### 10.3.3.4 Nucleotide Codes Table

PatentIn v. 2.0 uses the following nucleotide symbols:

  ------- --------------------- -----------------------------------------
  Code    Group                 Nucleotide(s)

  A       a                     **A**denine

  C       c                     **C**ytosine

  G       g                     **G**uanine

  T       t                     **T**hymine (in DNA)

  U       u                     **U**racil (in RNA)

  Y       c or t(u)             P**y**rimidine

  R       a or g                Pu**r**ine

  M       a or c                A**m**ino

  K       g or t(u)             **K**eto

  S       g or c                **s**trong interaction (3 hydrogen bonds)

  W       a or t(u)             **w**eak interaction (2 hydrogen bonds)

  H       a or c or t(u)        not-G

  B       g or t(u) or c        not-A

  V       g or c or a           not-T or not-U

  D       g or a or t(u)        not-C

  N       g,a,c or t(u)         A**n**y
  ------- --------------------- -----------------------------------------

#### 10.3.3.5 Amino Acid Codes Table

PatentIn v. 2.0 uses one-letter amino acid in its Sequence Editor. They
will appear in the printed sequence listing for features that require
three letter amino acids.

**NOTE**: The three-letter code is shown here for reference. It is
[not]{.underline} used in the PatentIn v. 2.0 Sequence Editor at any
time.

  ------------------------------------------------------------------------
  One-Letter Code  Three-Letter Code Amino Acid
  ---------------- ----------------- -------------------------------------
  A                Ala               Alanine

  R                Arg               Arginine

  N                Asn               Asparagine

  D                Asp               Aspartic acid

  C                Cys               Cysteine

  Q                Gln               Glutamine

  E                Glu               Glutamic acid

  G                Gly               Glycine

  H                His               Histidine

  I                Ile               Isoleucine

  L                Leu               Leucine

  K                Lys               Lysine

  M                Met               Methionine

  F                Phe               Phenyalanine

  P                Pro               Proline

  S                Ser               Serine

  T                Thr               Threonine

  W                Trp               Tryptophan

  Y                Tyr               Tyrosine

  V                Val               Valine

  B                Asx               Aspartic acid or Asparagine

  Z                Glx               Glutamic acid or Glutamine

  X                Xaa               Any amino acid
  ------------------------------------------------------------------------

## Exiting

When you have finished entering the sequence information, click either
the **Save** or **Exit** buttons. If you click on the **Save** button,
the information entered is saved to the current application. If you
click on the **Exit** button, the program will automatically save the
entered information, then return to the Sequence Data browse screen.

## Reordering Sequences

PatentIn offers an easy way to re-arrange the order of sequences within
the Sequence Listing by using the standard "Drag and Drop" mouse
function.

Within the *Sequence Data Browse Screen*, left click on the sequence
that you wish to move. [While holding the left mouse button
down]{.underline}, drag the sequence to the position within the list
where you wish to place the sequence. You will notice an icon of a hand
moving the sequence to its new location.

**NOTE**: The numerical order of the sequences within the Sequence Data
Browse Screen denotes the order in which sequences are compiled in the
Sequence Listing. The order number does not necessarily denote the
actual SEQ ID NO order. If a sequence had previously been deleted (using
the delete button on the screen), or a sequence has a CDS feature, which
will in turn generate a protein sequence, the SEQ ID NO assigned to a
sequence in a compiled Sequence Listing will not correspond to the order
number shown in the list.

## Code '000'

### Purpose

WIPO Standard ST.25, paragraph 5, states "Each sequence shall be
assigned a separate sequence identifier. The sequence identifiers shall
begin with 1 and increase sequentially by integers. If no sequence is
present for a sequence identifier, the code '000' should appear under
the numeric identifier \<400\>, beginning on the next line following the
SEQ ID NO."

The purpose of this clause is to permit flexibility in the preparation
and amendments of Sequence Listings. The characters 000 are the
language-neutral code meaning "This sequence is intentionally skipped."

In rare instances, this function may need to be used if, for instance,
the sequence numbering within the Sequence Listing or patent
application's specification is modified, and a SEQ ID NO is dropped. In
lieu of retyping the entire specification to accommodate a change in the
SEQ ID NO order, the "000" function can be used as a placeholder within
the Sequence Listing to preserve the current numbering.

The following example shows how sequence number 5 is intentionally
skipped:

\<210\> 5

\<400\> 5

000

**NOTE**: This differs from the "Delete" sequence button on the Sequence
Data Browse Screen. (See **Section 9.1.10** "Delete" for information on
this button). When the "Generate Sequence Listing" button is used, the
sequences that have been "deleted" by using the delete button on the
Sequence Data Browse Screen will never show up on the compiled Sequence
Listing. On the contrary, the "000" function is creating a **place
holder** for preserving a SEQ ID NO, and this will display on the
compiled Sequence Listing.

### 10.6.2 How to insert the "000" code 

If a sequence has already been included in the Sequence Listing, and it
is intended for that SEQ ID NO to display the "000" code, first select
the MODIFY button on the *Sequence Data Browse Screen.* Insert as the
[first three characters]{.underline} the code **000**. Then SAVE and
EXIT. See example below.

![](media/image18.wmf){width="6.65625in" height="4.0625in"}

[]{#__RefHeading___Toc424703421 .anchor}Figure 10-: Example of 000 Place
Holder

If a sequence has not already been entered, and a "000" placeholder
needs to be inserted, first click on ADD within the *Sequence Data
Browse Screen*. Then simply type **000** in place of the sequence. Then
SAVE and EXIT.

If the "000" placeholder ever needs to be removed, click on the Modify
button within the *Sequence Data Browse Screen*. Then delete the first
three **000** characters. Then SAVE and EXIT. When you are returned to
the Sequence Data Browse Screen, highlight the empty sequence and click
on the Delete button.

# 11. Completing the Feature Information

The Feature Information data entry screen is a vital part of PatentIn v.
2.0. It has been designed to enter simple features easily. The data
entry screen allows you to indicate biologically significant regions of
the sequence. Annotating the features of your sequence enhances the
utility of your data for other researchers.

The feature table is based exclusively based on Tables 5 and 6 within
WIPO ST 25. Any feature can be represented, including, but not limited
to, regions which:

-   are promoters,

-   are enhancers,

-   are an enzyme's catalytic site,

-   bind DNA,

-   bind protein,

-   result from recombination of different sequences,

-   are a recognizable repeated unit,

-   have secondary or tertiary structure,

-   exhibit variation, or

-   have been revised or corrected.

## 11.1 Feature Information Data Entry Screen {#feature-information-data-entry-screen .unnumbered}

Click on the **Feature** button in the Sequence Data browse screen to
access the Feature Information data entry screen. The organization and
interaction of the Feature Information data entry screen differs from
the other data entry screens in the program. The Feature Information
data entry screen is divided into three parts, as shown in **Figure
11-1**. These three parts are: **Data Entry Block, Other Information
Window,** and **Feature Location Window**.

![](media/image19.png){width="6.34375in" height="3.9819444444444443in"}

[]{#__RefHeading___Toc424703425 .anchor}Figure 11-: Feature Information
Data Entry Screen

### 11.1.1 Data Entry Block 

The Data Entry Block consists of specific fields located at the top of
the screen that display information about the feature that you are
entering. Use the Data Entry Block of the Feature Information data entry
screen to enter the type of feature and its location in the sequence.
The Data Entry Block includes the following four fields: a **Feature
Name/Key** field, a **From** field, a **To** field, and a **Complement**
field.

#### 11.1.1.1 Feature Name/Key

In this field, choose a keyword describing the feature from the pulldown
list. This pulldown list will differ depending upon the type of sequence
(i.e. nucleic acid versus protein). For more information on selecting
the Feature Name/Key, refer to **Section 11.2** "Choosing a Feature
Name/Key."

#### 11.1.1.2 From Field

The next field is the **From** field in which you must enter the
starting position of the feature.

#### 11.1.1.3 To Field 

The next field is the **To** field in which you must enter the ending
position of the feature.

#### 11.1.1.4 Complement Field

This field is used to indicate whether the feature is on the
complementary strand. If so, select "**C**" from the pulldown list.
Otherwise, leave blank or (if "C" has been selected) select the blank
entry from the list. When "C" is selected, the word "**Complement"**
appears in the Feature Location entry when saved.

**NOTE:** You should still specify locations on the complementary strand
in the increasing 5'-to 3' direction as if they were on the presented
strand. That is, the number of the **From** position should always be
less than that of the **To** position.

### 11.1.2 Other Information Window

The middle third of the screen contains a window in which you may enter
a more detailed description of the feature key. Use this **Other
Information** window to enter specific feature qualifiers.

### 11.1.3 Feature Location Window

This window in the bottom third of the screen is used to specify the
feature\'s location. For more information on the feature location, refer
to **Section 11.3** "Specifying the Feature's Location."

Figure 11-1 illustrates how features are displayed in the Feature
Location Window after they are saved. Special notation markers indicate
a complex location in your feature. The word **Complement,** placed in
front of any nucleic acid feature in which a **C** was entered in the
field, indicates that the feature is on the complementary strand.

## 11.2 Choosing a Feature Name/Key {#choosing-a-feature-namekey .unnumbered}

The data banks have developed a set of keywords that describe the major
features found in nucleic acid and protein sequences. These keywords are
referred to as feature keys. Feature keys indicate the biological nature
of the annotated feature or other versions of the sequence. Choosing the
appropriate feature key is important because these keys are frequently
used to find or retrieve similar features or features with related
functions.

PatentIn v. 2.0 provides lists of these feature keys; you must choose
the one that best describes the feature you are entering. The lists of
features differ depending upon whether your sequence is a nucleic acid
or a protein. PatentIn v. 2.0 automatically provides the list based on
the sequence type declared when the sequence was **Add**ed or
**Import**ed to PatentIn. If **DNA**, **RNA**, or **Combined DNA/RNA**
was used, PatentIn v. 2.0 allows you to enter nucleic acid features; if
a **PRT code** was used, you will be able to enter protein features.

### 11.2.1 Specific Feature Keys

With the cursor in the **Feature Name/Key** field, click in the field to
see a list of feature keys.

Choose **misc_feature** if you cannot find a key that matches the
feature you want to enter. Further define the misc_feature in the
"**Other Information**" window. In the event that you wish to only
insert text (free text) in the "**Other Information**" window, select
the **dash** (-) feature. Selecting **place holder** (-) automatically
enters "N/A" in both the **From** and **To** fields.

See **Sections 13.1** and **13.2** for listings of other valid Feature
Name keys.

### 11.2.2 Additional Information Button

If the selection in the **Feature Name/Key** field is **Mod_Base** for a
nucleic acid sequence, or **Mod_Res** or **LIPID** for an amino acid
sequence, pick lists are presented that permit additional features to be
defined for the selection as per WIPO ST. 25. The results of this
secondary selection appear in the Additional Information window.

When one of these features requiring additional features is selected,
the Additional Information button is also enabled. This Additional
Information button allows you to reenter the associated additional
feature picklist to change your entry. See Feature Key Additional
Descriptions for a list of the selection for each of the three features.

## 11.3 Specifying the Feature's Location

Once you have selected a feature key, you must indicate where in the
sequence the feature occurs. PatentIn version 2.0 permits you to enter
features that have single, distinct start and end points.

The feature location can be either a single residue or a contiguous span
of residues.

You can enter a location by typing the position of the first residue in
the feature in the **From** field and the position of the last residue
in the feature in the **To** field.

Some features have a single residue for their location. If this is the
case, enter the single position in both the **From** field and **To**
field. PatentIn will enter "N/A" in the **To** field once the feature is
saved.

Complex locations, such as "residues 9, 247, and 893, comprise the
catalytic site," may be entered by selecting "-" (dash) within the
**Feature Name/Key** field and typing the description of the complex
feature within the "**Other Information**" field \<223\>.

## 11.4 Saving the Feature

After you have entered the **Feature Key**, **Feature Location**, and
**Other Information,** click either the **Save** or **Exit** button. If
you click on the **Save** button, the information entered is saved to
the current application and the fields are cleared for the next feature.
If you click on the **Exit** button, the program will prompt you to save
the entered information, then returns you to the Sequence Data browse
screen. If you wish to interrupt the process of entering a feature
without exiting the screen, activating **Clear All** will clear all of
the data entry fields.

## 11.5 Receiving an Error or Warning Message When Saving - The Next Action to Take

If your sequence contains a CDS or EXON that cannot be evenly grouped
into codons (sets of three), PatentIn v. 2.0 displays an error message
reminding you that "The final nucleotide in coding region lies within a
codon" and instructs you to "revise the \<value\> in the **To** field."

## 11.6 Editing a Feature

If you wish to change a feature you have already entered, move the
cursor to the **Feature Location Window***.* Use the arrow keys to move
up or down within the list of features and position the cursor on the
tag assigned to the feature you wish to edit, then press **Enter** or
activate the **Edit Feature button**. You may also double-click on the
record to recall. The tag is found in the far-left column in the Feature
Location Window*.* These alphabetical characters are permanently
assigned sequentially by PatentIn from "a" to "zz" and do not change if
a feature is deleted. Thus, the maximum number of features per sequence
is 649.

The information pertaining to that feature appears in the Data Entry
Block and in the **Other Information Window***.* Make the necessary
changes, then save the feature according to the instructions provided in
**Section 11.4** "Saving the Feature."

## 11.7 Deleting a Feature

Before deleting a feature you have already entered, be sure to complete
and save the feature you are currently editing. The Data Entry Block
should be empty before deleting features.

If you wish to delete a feature that you have already entered, highlight
the feature in the **Feature Location Window** and either click the
**Delete** button or press the **Delete** key on the keyboard. The
program asks you to confirm that you really want to delete this feature.
If you answer **Yes,** the program deletes the feature. If you select
**No**, the program does not delete the feature.

## 11.8 Exiting the Feature Information Data Entry Screen

To exit the Feature Information data entry screen*,* you must first do
one of the following: Either save all features by clicking on the
**Save** button, or clear all fields by clicking on the **Clear All**
button, which will empty the Data Entry Block fields. Then **Exit**
normally.

## 11.9 Annotating a Protein Coding Region

If your sequence contains a protein coding region (CDS), you should
provide as much information about the features associated with that CDS
as possible. It is recommended that you add detailed comments in the
**Other Information Window**.

Describe a CDS on the Feature Information data entry screen by entering
the features associated with it in the following order:

1.  Select the feature "CDS" from the Feature Name/Key list.

```{=html}
<!-- -->
```
12. Enter the start and end position for the region to be translated in
    the **FROM** and **TO** fields.

13. Enter any additional information in the **Other Information**
    window.

14. Save.

15. If needed, a "mat_peptide" feature can be added to display where the
    mature peptide starts in the sequence. Enter the starting position
    in both the **FROM** and **TO** fields. **Save** and **Exit**.

**SEQUENCE LISTING**

**\<110\> Doe, John**

**\<120\> Title for sample Sequence Listing**

**\<130\> Docket No.123123**

**\<140\>**

**\<141\>**

**\<160\> 2**

**\<170\> PatentIn Ver. 2.0**

**\<210\> 1**

**\<211\> 154**

**\<212\> DNA**

**\<213\> Homo sapiens**

**\<220\>**

**\<221\> CDS**

**\<222\> (1)..(102)**

**\<220\>**

**\<221\> mat_peptide**

**\<222\> (43)**

**\<400\> 1**

**atg gcg aac aag ctc ttc ctc gtc tgc gca gct tgg agc cct gtg ttt 48**

**Met Ala Asn Lys Leu Phe Leu Val Cys Ala Ala Trp Ser Pro Val Phe**

**-10 -5 -1 1**

**cat cct cac cac cgc ttc cgt cta tcg cac cgt tgt cga gtt cca cga 96**

**His Pro His His Arg Phe Arg Leu Ser His Arg Cys Arg Val Pro Arg**

**5 10 15**

**aga ttg agacgccact aaccccatag gcccaataca gaaatgtcag aaggagtttt ca
154**

**Arg Leu**

**20**

**\<210\> 2**

**\<211\> 34**

**\<212\> PRT**

**\<213\> Homo sapiens**

**\<400\> 2**

**Met Ala Asn Lys Leu Phe Leu Val Cys Ala Ala Trp Ser Pro Val Phe**

**-10 -5 -1 1**

**His Pro His His Arg Phe Arg Leu Ser His Arg Cys Arg Val Pro Arg**

**5 10 15**

**Arg Leu**

**20**

## 11.10 Annotating an Internal Stop Codon in a Protein Coding Region

If a nucleic acid sequence contains a protein coding region (CDS), the
program will translate the CDS into its amino acid sequence in the
Sequence Listing. In the rare case that a CDS contains an internal stop
codon, you should follow the procedure below to annotate the region
properly. This procedure is necessary for the program to accurately
determine the numbering and length of the accompanying amino acid
sequence.

Include the internal stop codon in the location of the CDS. When the
program encounters an internal stop codon during translation, it places
a blank space below it and includes the internal stop codon in the
numbering and length calculation of the amino acid sequence (in this
case, 33 amino acids in length). The terminal stop codon is excluded
from the translation, numbering, and length of the amino acid sequence.

For example:

**ATG GCG AAC AAG CTC TTC CTC GTC TGC GCA GCT TGA GCC CTG TGT TTC 48**

**Met Ala Asn Lys Leu Phe Leu Val Cys Ala Ala Ala Leu Cys Phe**

**1 5 10 15**

**ATC CTC ACC ACC GCT TCC GTC TAT CGC ACC GTT GTC GAG TTC CAC GAA 96**

**Ile Leu Thr Asn Ala Ser Val Tyr Arg Thr Val Val Glu Phe Asp Glu**

**20 25 30**

**GAT TGA GACGCCAGTA ACCCCATAGG CCCAATACAG AAATGTCAGA AGGAGTTTCA 152**

**Asp**

## 11.11 Example of Sequence Annotation

PatentIn v. 2.0 sequence file.

In the example above, PatentIn V. 2.0 will create 2 protein sequences
below this DNA sequence. The first protein will include amino acid
proteins 1 through 11. (**Met** through **Ala**). The second amino acid
sequence that is generated will include positions 13 through 33 (**Ala**
to **Asp**).

**\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^\^**

**\<220\>**

**\<221\> CDS**

**\<222\> (1)..(102)**

**\<400\> 1 atg gcg aac aag ctc ttc ctc gtc tgc gca gct tga gcc ctg tgt
ttc 48 Met Ala Asn Lys Leu Phe Leu Val Cys Ala Ala Ala Leu Cys Phe 1 5
10 15**

**atc ctc acc acc gct tcc gtc tat cgc acc gtt gtc gag ttc cac gaa 96**

**Ile Leu Thr Thr Ala Ser Val Tyr Arg Thr Val Val Glu Phe His Glu**

**20 25 30**

**gat tga gacgccacta accccatagg cccaatacag aaatgtcaga aggagttttc a 153**

**Asp**

**\<210\> 2**

**\<211\> 11**

**\<212\> PRT**

**\<213\> Homo sapiens**

**\<400\> 2**

**Met Ala Asn Lys Leu Phe Leu Val Cys Ala Ala**

**1 5 10**

**\<210\> 3**

**\<211\> 21 \<212\> PRT \<213\> Homo sapiens**

**\<400\> 3 Ala Leu Cys Phe Ile Leu Thr Thr Ala Ser Val Tyr Arg Thr Val
Val 1 5 10 15 Glu Phe His Glu Asp 20**

# 12. Generate an Application Sequence Listing

## 12.1 Generating the Sequence Listing

When you have entered your sequence, along with all the relevant
annotation and biological information, you can prepare the Sequence
Listing that will be submitted to the receiving office. Follow the steps
below to generate the Sequence Listing.

1.  Select Generate Sequence Listing from the *Sequence Functions*
    submenu, or select "Generate Sequence Listing" from the *Quick
    Guide.*

```{=html}
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```
16. PatentIn v. 2.0 verifies that the values have been entered in the
    general information-related fields that are mandatory for the
    Sequence Listing. If any of the mandatory information is missing,
    the program warns you that there are missing items and displays a
    list of missing items. (Refer to **Section 6.2** "Mandatory Fields
    in Data Entry Screens").

17. If there are errors return to the appropriate screen(s) or the
    Sequence Editor and supply the missing data. Recreate the sequence
    listing by repeating steps 1 and 2.

18. After you have filled in all the mandatory fields, PatentIn v. 2.0
    begins to compile the Application Sequence Listing and displays the
    message: "***Gathering Application Information, please wait\...***"

If your sequence contains a CDS with an internal stop codon, the program
displays a warning that it found an internal stop codon in the coding
region, and then continues with the translation. If your CDS should NOT
contain an internal stop codon, you may need to return to the Sequence
Editor to check that the sequence is correct, or to the Feature
Information data entry screen to check that the CDS was entered
correctly. If your CDS actually does include an internal stop codon,
select the **OK** button within the pop-up warning messages, and the
system will proceed in building the Sequence Listing.

**NOTE**. If you make any changes to your application, you will need to
recreate the Sequence Listing from the beginning by selecting **Generate
Sequence Listing** from the Quick Guide.

## Browse Sequence Listing

Once the sequence is compiled after selecting the **Generate Sequence
Listing** option, the complete Sequence Listing file will appear. From
the "View Listing" window, the user may **Print, Copy to Disk,** or
**Exit**. (If error messages are displayed at the top of the Sequence
Listing, the user will be unable to copy the file to a disk.)

If a file has previously been through the **Generate Sequence Listing**
function**,** and the Sequence Listing is error-free, the last selection
on the *Quick Guide*, **Browse, Print, or Copy Sequence Listing** can be
used. The purpose of having a separate option for browsing, printing,
and copying an error free sequence listing is to avoid generating the
Sequence Listing again. That can be a long process for a big file.

## 12.3 Printing the Sequence Listing

PatentIn v. 2.0 stores the Application Sequence Listing in a file called
*FILENAME*. APP. This is an ASCII file without page breaks so that the
file can be printed on the widest variety of printers. You can print
this file as the paper version of the application. This option is
available in two places: the **Generate Sequence Listing** option and
the **Browse, Print, or Copy Sequence Listing** option from the Browse
Sequence Listing. To print, click on the print button and make your
selection in the print dialog box.

WIPO ST.25 paragraph 3 requires that you submit a paper copy of your
.APP file as part of your patent application. To aid the user in
complying with the paper copy requirements of the Sequence Listing,
PatentIn provides a function that numbers the printed pages. Since some
receiving offices do not allow numbered pages (e.g., JPO), PatentIn v.
2.0 gives the user the selection to print with or without printed page
numbers.

To change the default paper size in your printer, adjust the settings in
your Windows Control Panel.

## 12.4 Editing the Sequence Listing

After you have generated the Sequence Listing, you should print the file
and review it for accuracy. If information is missing or incorrect,
supply or correct the information, then re-compile the Sequence Listing
via the **Generate Sequence Listing** function.

**CAUTION:** Do [NOT]{.underline} open the .APP file into a word
processor. All editing must be done in an ASCII editor. A word processor
will change the font and margins settings and therefore change the
format of the output. It is suggested that you use the DOS "Edit"
feature. Directions: Open a MSDOS Shell Command (COMMAND.COM), and at
the prompt, type in the **EDIT** and the path to the file.\
(i.e. **EDIT C:\\PATIN2\\SAMPLE\\ SAMPLE.APP.)**

After editing your file, select, **Save**, then **Exit** (within the
file pulldown menu). This is the fastest, safest way to edit an ASCII
file, and will not interfere with PatentIn's formatting.

Notepad is also universally available within Windows™. In Windows 3.x,
if Notepad is not in a Windows group, execute it from within the File
Manager (which is a standard item in the Main group). The NOTEPAD.EXE
file is in the Windows subdirectory. In Windows 95 and NT, it is on the
Task Bar under the accessories. Open the .APP file as with any other
Windows application. Notepad, like DOS EDIT, will not affect the
formatting of the file.

**CAUTION:** In Notepad, if the file is saved to another directory using
the "Save As" feature, ensure that the file is saved with the "Save as
[t]{.underline}ype" feature set to "All Files" to avoid a .TXT file
extension.

## 12.5 About Sequence Listing Output

If the Sequence Listing contains a nucleotide sequence, PatentIn v. 2.0
groups bases in sets of 10 with 60 bases per line in the sequence
output, except where coding regions are indicated. In coding regions,
PatentIn v. 2.0 groups bases by three into codons with 16 codons per
line.

If the Sequence Listing contains a protein sequence, PatentIn v. 2.0
places 16 amino acids per line in the sequence output.

If you select a DNA or RNA sequence that contains protein coding regions
(CDS regions) for the Sequence Listing, PatentIn v. 2.0 translates the
CDS; the corresponding three-letter amino acid code appears below each
codon in the sequence output. In addition, the program automatically
appends the three-letter amino acid translation of each CDS to the
Sequence Listing as a separate sequence immediately following the
nucleic acid sequence having the CDS feature. If you select one sequence
with three CDS regions, your Sequence Listing will contain four
sequences: the original nucleic acid sequence you selected, and the
translated amino acid sequence comprising the three CDS regions.

If the application contains an amino acid sequence, the one-letter code
used by the Sequence Editor will be converted to three-letter amino acid
code in the output.

### 12.5.1 Numbering Sequence Listing Residues in the Output

For Sequence Listings that contain nucleic acids, PatentIn Version 2.0
counts the number of bases in each line, from the first base to the last
base in the sequence, and places this number in the right margin of the
sequence output. For Sequence Listings that contain amino acid
sequences, PatentIn Version 2.0 numbers every fifth residue, beginning
with the first amino acid, and places this number below the residue in
the sequence output.

If the nucleic acid sequence contains a CDS region, PatentIn Version 2.0
numbers the first amino acid of the CDS region as 1. If the sequence
contains multiple non-overlapping CDS regions, the program translates
and numbers each CDS region independently. Each CDS translation then
appears as a separate sequence in the output. In the rare case of
overlapping CDS regions, the program will include only the first
overlapping CDS region listed in the feature table in the sequence
output. You will need to enter and save the remaining overlapping CDS
regions as separate sequences in the Sequence Editor and include each
one in the Sequence Listing.

If the CDS region includes a mat_peptide feature, the program numbers
the first amino acid of the **mat_peptide** as 1, with negative numbers
to the left (amino-terminal direction), extending to the beginning of
the CDS. If the CDS contains multiple **mat_peptides,** the program
numbers the first amino acid of the 5'-mat **mat_peptide** as 1.

## 12.6 Information on How Data is Stored

All of the patent annotation and feature information is stored in a file
with the same name you assigned to the application, followed by the file
name extension .APP. Sequence data is stored in files with the extension
.GBS. PatentIn v. 2.0 uses these two files to create the
computer-readable output file that will be sent to the receiving office
as the Application Sequence Listing.

## 12.7 Final Steps

1.  Copy the Sequence Listing to selected medium (diskette).

```{=html}
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```
19. Print out Sequence Listing (preferably using page numbers), on
    appropriate sized paper. PCT requires A4 paper other receiving
    offices (e.g. US PTO) accept 8 ½" x 11" paper.

20. Submit diskette and paper copy of Sequence Listing to appropriate
    receiving office.

# 13. Reference

## 13.1 Feature Keys - Nucleic Acid

To select a feature key (in the Feature Information data entry
screen)*,* activate the Feature Name/Key pulldown list. The features on
the list are arranged alphabetically to facilitate access, but the
following section lists each feature on this list by category in order
to demonstrate their biological relationships.

**Feature Key Categories**

**RNA, transcript, and gene regions**

***Table 5*: *List of Feature Keys Related to Nucleotide Sequences***

  ----------------- ----------------------------------------------------------
  Key               Description

  Allele            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)

  misc\_            feature sequence is different from that presented in the
                    entry and cannot be

  difference        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)

  misc_structure    any secondary or tertiary structure or conformation 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)

  prim\_            primary (initial, unprocessed) transcript; includes 5\'
                    clipped region (5\'clip),

  transcript        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
                    permissable

  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

  transit_peptide   transit peptide coding sequence; coding sequence for 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\'clip           5\'-most region of a precursor transcript that is clipped
                    off during processing

  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 \[ \]
  ----------------- ----------------------------------------------------------

## 13.2 Feature Keys - Amino Acid

*Table 6: List of Feature Keys Related to Protein Sequences*

  --------------------------------------------------------------------------
  Key                     Description
  ----------------------- --------------------------------------------------
  CONFLICT                different papers report differing sequences

  VARIANT                 authors report that sequence variants exist

  VARSPLIC                description of sequence variants produced by
                          alternative splicing

  MUTAGEN                 site which has been experimentally altered

  MOD_RES                 post-translational modification of a residue

  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   of asparagine, aspartic acid, proline or lysine
  ACID HYDROXYLATION      

  METHYLATION             generally of lysine or arginine

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

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

  SULFATATION             generally of tyrosine

  LIPID                   covalent binding of a lipidic moiety

  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

  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

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

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

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

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

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

  SIGNAL                  extent of a signal sequence (prepeptide)

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

  PROPEP                  extent of a propeptide

  CHAIN                   extent of a polypeptide chain in the mature
                          protein

  PEPTIDE                 extent of a released active peptide

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

  CA_BIND                 extent of a calcium-binding region

  DNA_BIND                extent of a DNA-binding region

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

  TRANSMEM                extent of a transmembrane region

  ZN_FING                 extent of a zinc finger region

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

  REPEAT                  extent of an internal sequence repetition

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

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

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

  ACT_SITE                amino acid(s) involved in the activity of an
                          enzyme

  SITE                    any other interesting site on the sequence

  INIT_MET                the sequence is known to start with an initiator
                          methionine

  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

  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

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

## 13.3 Feature Keys - Additional Descriptions

Any information required by WIPO ST. 25 or any information that the user
may wish to include clarifying a feature should be typed into the
Additional Information Window before storing the feature.

For **mod_res, modified_base,** and **lipid** features the following
additional qualifiers are presented as selection lists. The selections
may be changed by activating the **Add'l Information** button, which is
displayed with these features.

  -----------------------------------------------------------------------
  Feature: **MOD_RES** (modified residue)

  ACETYLATION

  AMIDATION

  BLOCKED

  FORMYLATION

  GAMMA_CARBOXYGLUTAMIC ACID

  METHYLATION

  PHOSPHORYLATION

  PYRROLIDONE CARBOXYLIC ACID

  SULFATATION
  -----------------------------------------------------------------------

  -----------------------------------------------------------------------
  Feature: **LIPID**

  PALMITATE

  FARNESYL

  GERANYL-GERANYL

  GPI-ANCHOR

  N_ACYL DIGLYCERIDE
  -----------------------------------------------------------------------

  -----------------------------------------------------------------------
  Feature: **Modified_base**

  Abbrv. Full description

  ac4c 4-acetylcytidine

  chm5u 5-(carboxyhydroxylmethyl)uridine

  cm 2\'-O-methylcytidine

  Cmnm5s2u 5-carboxymethylaminomethyl-2-thiouridine

  cmnm5u 5-carboxymethylaminomethyluridine

  d dihydrouridine

  fm 2\'-O-methylpseudouridine

  gal q beta, D-galactosylqueosine

  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-mannosylqueosine

  mcm5s2u 5-methoxycarbonylmethyl-2-thiouridine

  Mcm5u 5-methoxycarbonylmethyluridine

  mo5u 5-methoxyuridine

  ms2i6a 2-methylthio-N6-isopentenyladenosine

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

  mt6a N-((9-B-D-ribofuranosylPu-6-yl)N-methylcarbamoyl)threonine

  mv uridine-5-oxyacetic acid-methylester

  o5u uridine-5-oxyacetic acid (v)

  osyw wybutoxosine

  p pseudouridine

  Q queosine

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

## List of Numeric Heading Definitions

\<110\> Applicant

\<120\> Title of invention

\<130\> File reference

\<140\> Current patent application

\<141\> Current filing data

\<150\> Earlier patent application

\<151\> Earlier application filing date

\<160\> Number of SEQ ID NOs

\<170\> Software

\<210\> Information for SEQ ID NO:# (show sequence \# only)

\<211\> Length

\<212\> Type

\<213\> Organism

\<220\> Feature (main heading)

\<221\> Name/Key

\<222\> Location

\<223\> Other Information

\<300\> Publication Information (main heading)

\<301\> Authors

\<302\> Title

\<303\> Journal

\<304\> Volume

\<305\> Issue

\<306\> Pages

\<307\> Date

\<308\> Database name/accession number

\<309\> Database entry date

\<310\> Document number

\<311\> Filing date

\<312\> Publication date

\<313\> Relevant residues FROM .. TO ..

\<400\> Sequence (sequence shown under line after sequence #)

000 Annotation 39

Add 17, 18, 21, 22, 23, 26, 29, 30, 31, 33

Add'l Information Button 44, 58

Amino Acid Codes 38

Applicant Information 17

Applicant Information Browse Screen 18

Application Number 20

Artificial Sequence 25

Author Information 29

Browse Screen

Applicant Information 18

Prior Application Information 22

Clear All Button 45

Complement Field 43

Create New Application 9

Current Application Information Menu Option 6

Dash Feature 44

Data Entry Block 42

Data Entry Screen 6

Applicant Information 17

Application 6

Author Information 29

Current Application Information 19

Cursor Control Keys 7

Feature Information 25, 41, 46

Help 16

Maneuvering 7

Prior Application Information 20

Sequence Functions 7

Delete 17, 18, 21, 22, 23, 29, 31, 33

DNA Filter 32, 35

End Page Field 28

Error Message 45

Exit 17, 18, 20, 22

Feature 7, 8, 23, 25, 33, 37, 41, 42, 43, 44, 45, 46, 49, 53, 56, 58

Feature Button 41

Feature Information 41, 45

Data Entry Screen 25

Feature Information Data Entry Screen

Data Entry Line 42

Feature Location Window 43

Other Information Window 43

Feature Key Categories 53

Feature Key Descriptions 44, 56, 58

Feature Keys

Nucleic Acid 53

Feature Name/Key Field 42, 43

Field

Application Number 20

Complement 43

Completing 14

End Page 28

Feature Name/Key 42, 43

File Reference 9, 20

Filing Date 20

First Name 17

From 28, 42

Issue 28

Last Name 17

Mandatory 14

Middle Initial 18

Publication Date 28

Publication Name 28

Publication Type 27

Relevant Residues 28

Start Page 28

Suffix 17

Title 20, 28

To 29, 42

Volume 28

File Reference Field 9, 20

Filing Date Field 20

Filters 32, 36

DNA 32, 35

PRT 32

RNA 32, 35

Find *See* Sequence Editor, Search Menu

From Field 28, 42

Generate Sequence Listing 11, 39, 49, 50

Help 16

Import 23, 32

Individual 17

Installation 3

Internal Stop Codon 47

Issue Field 28

Language Preference 9

Languages 1

Library of Previously Defined Publications 30

Limitations 8

List of Feature Keys Related to Nucleotide Sequences 53

List of Feature Keys Related to Protein Sequences 56

Lists

Cursor Control Keys 7

Restricted Vocabulary 14

Main Menu 6

Main Menu/Quick Guide 11, 13

Mandatory Fields 14

Mat_peptide 51

Menu

Exit 12

Help 16

Main 6, 11

Main/Quick Guide 11

Modify 17, 18, 21, 22, 23, 26, 29, 30, 31, 33

New *See* Sequence Editor, File Menu

New Application 9

Next *See* Sequence Editor, Search Menu

Next Button 26

Nucleotide Codes 37

Numbering Sequence Listing Residues in the Output 51

Open *See* Sequence Editor, File Menu

Order *See* Sequence Editor

Organism 7, 14, 15, 23, 24, 25, 37

Other 25

Sequence 25

Unknown 25

Organization 17

Other Organism 25

Prior Application Information 20

Prior Application Information Menu Option 6

Protein Coding Region (CDS) 45, 47, 51

PRT Filter 32, 35

PRT One-Letter Filter 32, 35

PRT Three-Letter Filter 33, 35

Publication Date Field 28

Publication Name Field 28

Publication Type Field 27

Publications 7, 14, 23, 25, 30, 31, 33, 37

Regions

*Gene* 53

*RNA* 53

*Transcript* 53

Relevant Residues 28

Reordering *See* Sequence Editor

Restore 23, 31, 33

RNA Filter 32, 35

Save *See* Sequence Editor, File Menu

Feature Information 44, 45

Save As *See* Sequence Editor, File Menu

Search String *See* Sequence Editor, Search Menu

Sequence Annotation 47

Sequence Data Browse Screen 23

Sequence Editor 23, 29, 34, 51

Accessing 35

Data Entry Block 45

Feature Location Window 45

File Menu 35

Menu Bar 34

Order 23

Other Information Window 45

Reordering 39

Search Menu 37

Sequence Entry Window 34

Sequence Entry Window 34

Sequence Listing 49

Browse 7, 50

Editing 50

Generate 7

Generate 49

Output 50

Printing 50

Specific Feature Keys 43

Start Page Field 28

System Requirements 2

Table 5 53

Table 6 56

Title Field 20, 28

To Field 28, 42

Unknown Organism 25

Volume Field 28

Warning Message 45

WIPO ST.25 1, 25, 50