[Note: This version is known to be outdated; use with care.]

Table of Contents

1.1. Intended Audience

1.2.1. Conventions

1.2.2. HTML Format

1.2.3. LATEX Format

1.2.4. RTF Format

1.2.5. Exercises

1.3.1. Electronic Access

1.3.2. Site Adaptation

1.3.3. Printed Version and Publisher Information

1.3.4. Printed Version, Conditions of Use

2.1. Needed Equipment

2.1.1. Desktop

2.1.2. On-Site or Remote Central Computing Facilities

2.1.3. Prices

2.2.1. Local Site Information for Access:

2.3.1. User Name

2.3.2. Password

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

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

3.2.2. Problems on Ethernet

3.2.3. Communication Problems on Various Configurations

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

3.4.1. 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

3.5.1. 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

3.6.1. 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

4.2.1. Input

4.2.2. Parameters

4.2.3. Output

4.3.1. Calling the GCG Setup Program

4.4.1. Purpose of WPI

4.4.2. WPI Details: The Concept of "Lists"

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

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

4.4.5. Interaction of WPI Windows

4.4.6. Starting WPI

4.4.7. WPI and the User

4.5.1. ... Using WPI

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

4.5.3. Plotting Setup from the Command Line Using Generic Commands

4.5.4. Verification of the Plotting Environment

4.9.1. USENET NEWS

4.9.2. BIOSCI BULLETIN BOARDS

4.9.3. Frequently Asked Questions

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. Remote UNIX Copy

5.1.4. 'kermit'

5.1.5. ZMODEM

5.2.1. Navigation

5.2.2. Manipulation

5.2.3. Output

5.2.4. Local Site Information for Printing

5.3.1. Start the 'vi' Editor

5.3.2. Typing Text

5.3.3. Help for Sophisticated Functions

5.3.4. Screen Refresh

5.3.5. Exit the Editor

5.4.1. 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

6.2.1. 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

6.3.1. View Data on the Screen

6.3.2. Copy Data to Your Directory

6.4.1. The 'Mail' Program in UNIX

6.4.2. The 'mh' Program in UNIX

7.1. Principle of the 'seqed' Program

7.2.1. Start of the 'seqed' Program

7.2.2. Non-Sequence Information

7.2.3. Sequence Information and Exit

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

7.4.1. Conversion in between GCG formats

7.4.2. Problems in reformatting

8.1. Prerequisites for all examples and instructions

8.1.1. Text Output

8.1.2. Graphic Output, Launched via Command Line

8.1.3. Graphic Output, Launched via WPI

8.1.4. Notes on Graphics

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

8.3.1. Principle

8.3.2. 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

8.5.1. DNA to Protein

8.5.2. Protein to DNA

8.5.3. DNA to RNA and Vice Versa

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

8.7.1. 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

9.2.1. Comparison Calculation

9.2.2. Display Program

9.2.3. Detection of Internal Repeats

9.3.1. Motivation

9.3.2. Letter-by-Letter Alignment Prerequisites

9.3.3. Symbol Comparison Tables

9.3.4. Alignment Path Matrices

9.4.1. 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, Text

9.4.5. Programs to Display Two Aligned Sequences, Graphics

9.4.6. Significance Evaluation

10.1. Pattern Principles

10.1.1. Example of Pattern Benefit

10.1.2. Definition of a Pattern Language

10.2.1. Iterative Schedule

10.2.2. Considerations: Pattern Sensitivity

10.3.1. The 'findpatterns' Program

10.3.2. A PROSITE Database Searching Program

10.3.3. Other Pattern Motif Databases

11.1. Tools for Sequence Searching

11.1.1. Sensitive searching, using special computers

11.1.2. Extremely fast searching, using approximations

11.2.1. Principle of Similarity Detection

11.2.2. Expectations

11.2.3. Programs

11.3.1. Principle

11.3.2. Programs

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

11.5.1. 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, Time Effects and Location

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

12.2.1. 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

12.3.1. Creation of a Tree

12.3.2. PAUP-based Methods

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

13.2.1. Account

13.2.2. Equipment

13.2.3. Local Area Network

13.3.1. Internet

13.3.2. 'ftp'

13.3.3. 'HASSLE'

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

13.5.1. 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

14.1.

This document was written with the multi-format authoring tool JAMF (Just Another Metafile).

Publisher Information: Verlag Ute Doelz, FAX +41 61 6419012