JAMF Archive BioCompanion as published in 1995 THIS IS THE REFERENCE CODE AS PUBLISHED. Doelz, R. Optimal production of biological documentation: the JAM format. Comput. Applic. Biosci. 11, 224-226 (1995). The version you are currently viewing is the one printed and distributed via the Internet from the server of BioComputing Basel. Version 3.1 of the BioCompanion was published with version 2 of the JAMF software. The server that was indicated in the documentation has ceased to exist. Version 3.2 of the BioCompanion was not publicly available for free but was shareware that was distributed with GCG's software release 9. For the purpose of enhanced editing, JAMF was partially rewritten and the proprietary version 3.x of JAMF was used from 1996 onwards. The Biocompanion is available in a current version from the publisher . It has significantly changed both in software and content.
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Table of Contents

1.1. Intended Audience

1.2. How to Use this Guide

1.2.1. Conventions

1.2.2. HTML Format

1.2.3. LATEX Format

1.2.4. RTF Format

1.2.5. Exercises

1.3. Copyright

1.3.1. Electronic Access: Private Use

1.3.2. Electronic Access: Institutional Use

1.3.3. Site Adaptation

1.3.4. Printed Version

1.3.5. Printed Version, Conditions of Use

1.4. Acknowledgements

2.1. Needed Equipment

2.1.1. Desktop

2.1.2. On-Site or Remote Central Computing Facilities

2.1.3. Prices

2.1.4. Local Site Information for Accounts (VMS Operating System):

2.1.5. Local Site Information for Accounts (UNIX Operating System):

2.2. In order to Connect...

2.2.1. Local Site Information for Access:

2.3. Once You Have Made the Connection ...

2.3.1. User Name

2.3.2. Password

2.4. If You Successfully Logged In

2.5. If You Need to Change Your Password

2.6. Disconnect from the Computer

2.6.1. Emergency Break: Serial Line

2.6.2. Emergency Break: 'rlogin'

2.6.3. Emergency Break: 'telnet'

2.6.4. Emergency Break: 'set host'

2.6.5. Emergency Break: PC / Macintosh

3.1. No Response: No Window or Dark Screen

3.1.1. Technical Problems

3.1.2. Configuration Problems

3.2. No or Wrong Response (Setup Worked Before)

3.2.1. Problems on Serial Lines (Modems, etc.)

3.2.2. Problems on Ethernet

3.2.3. Communication Problems on Various Configurations

3.3. No Connection to Remote Host

3.3.1. Communication Problems on Various Configurations

3.3.2. Communication Problems on DECnet

3.3.3. Communication Problems on TCP/IP

3.3.4. Connection Problems on X-Windows

3.4. No Successful Login

3.4.1. Local Problems on LAT

3.4.2. Local Problems on PCs

3.4.3. Remote Problems on VMS

3.4.4. Remote Problems on UNIX

3.4.5. Remote Account Problems

3.5. During Session: No or Strange Events

3.5.1. Unknown Terminal

3.5.2. Screen Accidentally Locked

3.5.3. Screen Occupied by another Program - no Reaction

3.5.4. Screen Occupied by another Program - Takes all Input

3.5.5. Keys Give Wrong Response

3.5.6. National Character Set

3.5.7. Need to Delete 'lock'-File

3.6. Problems Caused by User

3.6.1. Quota Exceeded

3.6.2. Need to Stop a Previous Session

3.6.3. Need to Stop a Print Session

4.1. Standard Environment

4.1.1. Material and Methods

4.1.2. Setup of the Text Screen

4.1.3. Using X-Windows across the Network

4.1.4. Calling the GCG Setup Program

4.2. Wisconsin Package Interface

4.2.1. Purpose of WPI

4.2.2. WPI Details: The Concept of "Lists"

4.2.3. More WPI Details: The Concept of an "Output Manager"

4.2.4. Even more WPI Details: The Concept of a "Job Manager"

4.2.5. Interaction of WPI Windows

4.2.6. Starting WPI

4.2.7. WPI and the User

4.3. Setup of the GCG Plotting Environment

4.3.1. ... Using WPI

4.3.2. Plotting Setup from the Command Line Using the 'setplot' Utility

4.3.3. Plotting Setup from the Command Line Using Generic Commands

4.3.4. Verification of the Plotting Environment

4.4. Computer On-Line Documentation

4.5. GCG On-Line Documentation (Command Line Version)

4.6. GCG On-Line Documentation (WPI Version)

4.7. ATLAS On-Line Documentation

4.8. SRS On-Line Documentation

4.9. Network Help

4.9.1. USENET NEWS

4.9.2. BIOSCI BULLETIN BOARDS

4.9.3. Frequently Asked Questions

4.10. Printed Documentation

4.11. Human Help

5.1. Transfer of Data in between Computers

5.1.1. 'ftp'

5.1.2. VMS Import from other VMS Hosts via DECnet

5.1.3. UNIX Import from other UNIX Hosts via Remote Copy

5.1.4. 'kermit'

5.1.5. ZMODEM

5.2. File Handling Commands on Various Operating Systems

5.2.1. Navigation

5.2.2. Manipulation

5.2.3. Output

5.2.4. Local Site Information for Printing

5.3. Local Site Information for Editing

5.3.1. Start the EDT Editor

5.3.2. Typing Text

5.3.3. Help for Sophisticated Functions

5.3.4. Screen Refresh

5.3.5. Exit the Editor

5.4. Import of Sequences to the GCG Package

5.4.1. Sequence Formats

5.4.2. Reformatting Sequences

6.1. Principle

6.1.1. Production of Databases

6.1.2. Contents of an Entry

6.1.3. Networks of Databases

6.1.4. Computer Networks

6.2. Obtaining Data from Local Databases

6.2.1. Using the GCG Software: 'lookup'

6.2.2. Using the GCG Software: 'stringsearch'

6.2.3. Find Sequences in the Databases with ATLAS

6.2.4. Find Sequences in the Databases with SRS

6.2.5. Find Sequences in the Databases with ENTREZ

6.3. View (Local) Sequence Data

6.3.1. View Data on the Screen

6.3.2. Copy Data to Your Directory

6.4. Using Electronic Mail to Get Sequences via Network

6.4.1. The 'MAIL' Program in VMS

6.4.2. The 'EAN' Program in VMS

6.5. Find Sequences in the Databases with 'gopher' (via network)

6.6. Find Sequences in the Databases with World Wide Web (via Network)

6.7. The SRSWWW System

6.7.1. Getting Started

6.7.2. Example: Searching Databases

7.1. Principle of the 'seqed' Program

7.2. Enter Your Sequence from Scratch

7.2.1. Start of the 'seqed' Program

7.2.2. Non-Sequence Information

7.2.3. Sequence Information and Exit

7.3. Modification of an Existing File or Database Sequence

7.3.1. Navigation

7.3.2. Start of the 'seqed' Program

7.3.3. Screen Mode Commands

7.3.4. Command Line Mode Commands

7.4. Reformatting from RNA, DNA, MSF or other GCG Formats

7.4.1. Conversion in between GCG formats

7.4.2. Problems in reformatting

8.1. Prerequisites for all examples and instructions

8.1.1. Options for result display

8.1.2. NOTICE

8.2. Composition-Counting Programs

8.2.1. Principle

8.2.2. Detailed View on the "windows" Technique

8.2.3. Programs

8.2.4. Effect of the Window Size in the 'window' Program:

8.2.5. EGCG Programs

8.3. Reading Frame Estimation Programs

8.3.1. Principle

8.3.2. Programs

8.4. Restriction Enzyme Mapping Programs

8.4.1. Principle of Patterns

8.4.2. Using the 'prime' Program to Predict Primers in a Pattern Approach

8.4.3. Principle of Restriction Enzyme Mapping in a Pattern Approach

8.4.4. Programs

8.5. Translation

8.5.1. DNA to Protein

8.5.2. Protein to DNA

8.5.3. DNA to RNA and Vice Versa

8.6. Protein Tools

8.6.1. Secondary Structure Prediction

8.6.2. Visualisation of Secondary Structure

8.6.3. Fragmentation

8.6.4. Isoelectric Point

8.6.5. Simplification of Protein Sequences

8.7. Hints on additional software

8.7.1. Benefits of additional software

8.7.2. Disadvantages

8.7.3. Data transfer and formatting

9.1. Schematic Comparison

9.1.1. Principle of Sequence Alignment

9.1.2. Principle of Dotplots

9.1.3. Dotplot Principle - Improved

9.1.4. Dotplot Principle - Improved Again

9.1.5. Interpretation of Dotplots

9.2. GCG's Implementation of Schematic Comparison

9.2.1. Comparison Calculation

9.2.2. Display Program

9.2.3. Detection of Internal Repeats

9.3. Principle of the Analytical Comparison of Two Sequences

9.3.1. Motivation

9.3.2. Letter-by-Letter Alignment Prerequisites

9.3.3. Symbol Comparison Tables

9.3.4. Alignment Path Matrices

9.4. Comparison Programs

9.4.1. Two Sequences of Similar Length

9.4.2. Two Sequences of Different Length

9.4.3. DNA and Protein Sequences

9.4.4. Programs to Display Two Aligned Sequences

9.4.5. Significance Evaluation

10.1. Pattern Principles

10.1.1. Example of Pattern Benefit

10.1.2. Definition of a Pattern Language

10.2. Creation of Patterns

10.2.1. Iterative Schedule

10.2.2. Considerations: Pattern Sensitivity

10.3. Programs

10.3.1. The 'findpatterns' Program

10.3.2. A PROSITE Database Searching Program

11.1. Tools for Sequence Searching

11.2. Sequence Searching with Heuristic Methods

11.2.1. Principle of Similarity Detection

11.2.2. Expectations

11.2.3. Programs

11.3. Rigorous Searching in the Twilight Zone

11.3.1. Principle

11.3.2. Programs

11.4. Searching Strategies

11.4.1. Tuning of your Sequence

11.4.2. Translate DNA

11.4.3. Tuning of the 'fasta' Parameter "word size"

11.4.4. Tuning of the 'fasta' Parameter "list size"

11.4.5. Statistics Analysis of Hits

11.4.6. Mapping Result Data

11.4.7. Analysis of Target Sequences

11.5. Use of Specific Searching Libraries

11.5.1. Database Sub-Libraries

11.5.2. Sequence Lists (formerly File Of Sequence Names (FOSN))

11.5.3. Multiple Sequence Files (MSF)

11.5.4. Lists within the Wisconsin Package Interface (WPI)

11.5.5. Impact of Electronic Networks and Time Effects

11.5.6. Creation of own Databases

12.1. Principle of Multiple Sequence Alignment

12.1.1. Prerequisites

12.1.2. Finding the Best

12.1.3. Grouping

12.1.4. Result Evaluation

12.1.5. Limitations

12.2. Programs to Deal with Multiple Sequences

12.2.1. Manual Editing with the Multisequence Editor

12.2.2. Manual Editing of Sequence Alignments

12.2.3. Manual Editing of File of Sequence Names

12.2.4. Automatic Creation of File of Sequence Names

12.2.5. Automatic Generation of a Multiple Sequence Alignment

12.2.6. Display of the Dendrogram Generated by the 'pileup' program

12.2.7. Presentation of the Alignment

12.2.8. Graphic Presentation of Similarity in the Alignment

12.2.9. Schematic Presentation Sequence Similarity

12.3. Phylogeny

12.3.1. Creation of a Tree

12.3.2. PAUP-based Methods

12.3.3. Other Packages

12.4. Manual Creation of Sequence Alignments

12.5. Profiles

12.5.1. Principle

12.5.2. Formats of Sequences

12.5.3. Profile Generation

12.5.4. Profile Searching

12.5.5. Profile Analysis

13.1. What is an Operating System?

13.1.1. VMS

13.1.2. UNIX: ULTRIX

13.1.3. UNIX: OSF/1

13.1.4. UNIX: SunOs

13.1.5. UNIX: Solaris

13.1.6. UNIX: IRIX

13.2. Technical Issues: Local Setup

13.2.1. Account

13.2.2. Equipment

13.2.3. Local Area Network

13.3. Technical Issues: Networking

13.3.1. Internet

13.3.2. 'ftp'

13.3.3. 'HASSLE'

13.4. Just Another Metafile Format (JAMF)

13.4.1. Motivation

13.4.2. Why no Translators?

13.4.3. Structure of this Document

13.4.4. JAMF Philosophy

13.4.5. Conditions of Use

13.5. JAMF Specification

13.5.1. Files

13.5.2. Input Flexibility: Customisation of Scope

13.5.3. Comment Statements

13.5.4. Conditional Statements

13.5.5. Conditions

13.5.6. Inclusion

13.5.7. Formatting Statements

13.5.8. Verbatim Formatting

13.5.9. Special Formatting

13.5.10. Emphasised Text

13.5.11. Reference Links

13.5.12. Line Breaks and Paragraphs

13.5.13. Page Break

13.5.14. Items and Lists of Items

13.5.15. Structuring Statements

13.5.16. Referencing Statements