Table of Contents

1.1 Needed Equipment

1.1.1. Desktop

1.1.2. On-Site or Remote Central Computing Facilities

1.1.3. Prices

1.2.1. Prerequisites

1.2.2. Needed Applications

1.2.3. Getting Launched

1.2.4. The Home Page

1.2.5. Working Effectively

1.2.6. Performance Issues

1.2.7. Panic recovery

1.2.8. Sophisticated use of the Web

1.2.9. WWW security

1.2.10. Difference to Interactive Sessions

1.3.1. Cabling

1.3.2. Desktop Equipment - Workstation Type

1.3.3. Hardcopy Devices

1.3.4. Local Site Information for Access:

1.4.1. User Name

1.4.2. Password

1.7.1. Regular operation

1.7.2. Emergency Break: Serial Line

1.7.3. Emergency Break: 'rlogin'

1.7.4. Emergency Break: 'telnet'

1.7.5. Emergency Break: 'set host'

1.7.6. Emergency Break: PC / Macintosh

1.8.1. Technical Problems

1.8.2. Configuration Problems

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

1.9.2. Problems on Ethernet

1.9.3. Communication Problems on Various Configurations

1.10.1. Communication Problems on Various Configurations

1.10.2. Communication Problems on TCP/IP

1.10.3. Connection Problems on X-Windows

1.11.1. Local Problems on LAT

1.11.2. Local Problems on PCs

1.11.3. Remote Problems on VMS

1.11.4. Remote Problems on UNIX

1.11.5. Remote Account Problems

1.12.1. Unknown Terminal

1.12.2. Screen shows lots of unreadable characters

1.12.3. Screen weird after graphics

1.12.4. Screen Accidentally Locked

1.12.5. Screen Occupied by another Program - no Reaction

1.12.6. Screen Occupied by another Program - Takes all Input

1.12.7. Keys Give Wrong Response

1.12.8. National Character Set

1.12.9. File Sharing problems

1.12.10. Need to Delete 'lock'-File

1.13.1. Quota Exceeded

1.13.2. Need to Stop a Previous Session

1.13.3. Need to Stop a Print Session

1.13.4. File accidentially deleted

2.1 Standard Environment

2.1.1. Material and Methods

2.1.2. Setup of the Text Screen

2.1.3. X-Windows principle

2.1.4. Usage of X Windows

2.2.1. Input

2.2.2. Required and Optional Parameters

2.2.3. Output

2.4.1. Purpose of SeqLab

2.4.2. The SeqLab Multiple Sequence Editor (SeqLab "edit mode")

2.4.3. SeqLab Details: The Concept of "Lists"

2.4.4. More SeqLab Details: The Concept of an "Output Manager"

2.4.5. Even more SeqLab Details: The Concept of a "Job Manager"

2.4.6. Interaction of SeqLab Windows

2.4.7. Starting SeqLab

2.4.8. SeqLab and the User

2.5.1. ... Using SeqLab

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

2.5.3. Plotting Setup from the Command Line Using Generic Commands

2.5.4. Verification of the Plotting Environment

2.9.1. USENET NEWS

2.9.2. BIOSCI BULLETIN BOARDS

3.1 Transfer of Data in between Computers

3.1.1. 'ftp'

3.1.2. DECnet Copy

3.1.3. Remote UNIX Copy

3.1.4. 'Kermit'

3.1.5. ZMODEM

3.2.1. PC/Mac File Sharing

3.2.2. Navigation on VMS and UNIX systems

3.2.3. Manipulation of VMS and UNIX files

3.2.4. Output on VMS and UNIX systems

3.2.5. Local Site Information for Printing

3.3.1. Start the 'vi' Editor

3.3.2. Typing Text

3.3.3. Help for Sophisticated Functions

3.3.4. Screen Refresh

3.3.5. Exit the Editor

3.4.1. Sequence Formats

3.4.2. Importing Sequences into SeqLab

3.4.3. Reformatting Sequences into GCG (via commandline)

3.4.4. PC / Mac Files

4.1 Principle

4.1.1. Production of Major Databases

4.1.2. Contents of a Sequence Database Entry

4.1.3. Scope of a Query

4.1.4. Networks of Databases

4.1.5. Computer Networks

4.2.1. Using the GCG Software: 'lookup'

4.2.2. Using the GCG Software: 'stringsearch'

4.2.3. The GCG Database Browser in SeqLab

4.2.4. Find Sequences in the Databases with SRS

4.2.5. Find Sequences in the Databases with ENTREZ

4.3.1. View Data on the Screen

4.3.2. Copy Data to Your Directory on the GCG host

4.4.1. Requirements

4.4.2. Gopher

4.4.3. WWW in Biology

4.5.1. Methods to collect similar entries

4.5.2. Paradigm to deal with multiple sequences

4.5.3. Programs to use several sequences simultaneously

5.1 Considerations

5.1.1. The Place Of Birth Changed

5.1.2. Use of programs other than the GCG package

5.1.3. Entering Data Is Serious

5.1.4. Related Programs

5.2.1. Basic Concepts

5.2.2. Steps required before typing a new sequence

5.2.3. Editing Sequences in SeqLab

5.4.1. Start of the 'seqed' Program

5.4.2. Non-Sequence Information

5.4.3. Sequence Information and Exit

5.4.4. Computational aids

5.5.1. Navigation

5.5.2. Start of the 'seqed' Program

5.5.3. Screen Mode Commands

5.5.4. Command Line Mode Commands

5.6.1. Conversion in between GCG formats

5.6.2. Problems in reformatting

5.7.1. Principle of Fragment Assembly

5.7.2. The Fragment Assembly Process

5.7.3. The Fragment Assembly Data Structures

5.7.4. GCG's implementation of the Fragment Assembly System

6.1 Prerequisites for all examples and GCG programs

6.1.1. Text Output

6.1.2. Graphic Output, Launched via Command Line

6.1.3. Graphic Output, Launched via SeqLab

6.1.4. Notes on Graphics

6.2.1. Principle of alphabets

6.2.2. Principle of counting sequence ( -properties)

6.2.3. Detailed View on the "windows" Technique

6.2.4. Programs

6.2.5. Effect of the Window Size

6.3.1. Principle

6.3.2. GCG Programs for reading frames

6.3.3. Methods to verify the reading frame by sequence searching

6.4.1. Principle of Patterns

6.4.2. Using Programs to Predict Primers in a Pattern Approach

6.4.3. Principle of Restriction Enzyme Mapping in a Pattern Approach

6.4.4. Programs

6.5.1. DNA to Protein

6.5.2. Protein to DNA

6.5.3. DNA to RNA and Vice Versa

6.6.1. Secondary/Tertiary Structure Prediction

6.6.2. Schematical Visualisation of Secondary Structure

6.6.3. Fragmentation

6.6.4. Isoelectric Point

6.6.5. Simplification of Protein Sequences

6.7.1. Benefits of additional software

6.7.2. Disadvantages

6.7.3. Data transfer and formatting

7.1 Schematic Comparison

7.1.1. Principle of Sequence Alignment

7.1.2. Principle of Dotplots

7.1.3. Dotplot Principle - Improved

7.1.4. Dotplot Principle - Improved Again

7.1.5. Interpretation of Dotplots

7.2.1. Comparison Calculation

7.2.2. Display Program

7.2.3. Analysis of genomic sequences

7.2.4. Detection of Internal Repeats

7.3.1. Motivation

7.3.2. Letter-by-Letter Alignment Prerequisites

7.3.3. Symbol Comparison Tables

7.3.4. Alignment Path Matrices

7.4.1. Information content

7.4.2. Automatic translation on the fly

7.5.1. Using Sequence Comparison in SeqLab

7.5.2. Two Sequences of Similar Length

7.5.3. Two Sequences of Different Length

7.5.4. Two Overlapping Sequences

7.5.5. Two Sequences of Very Different Length

7.5.6. DNA and Protein Sequences

7.5.7. Programs to Display Two Aligned Sequences as Text

7.5.8. Programs to Display Two Aligned Sequences as Graphics

7.5.9. Significance Evaluation

8.1 Pattern Principles

8.1.1. Example of Pattern Benefit

8.1.2. Definition of a Pattern Language

8.1.3. Drawbacks of patterns

8.2.1. Iterative Schedule

8.2.2. Considerations: Pattern Sensitivity

8.3.1. The 'findpatterns' Program

8.3.2. A PROSITE Database Searching Program

8.3.3. Other Pattern Motif Databases

9.1 Tools for Sequence Searching

9.1.1. Sensitive searching, using special computers

9.1.2. Extremely fast searching, using approximations

9.2.1. Principle of Similarity Detection

9.2.2. Expectations

9.2.3. Programs

9.3.1. Principle

9.3.2. Programs

9.4.1. Tuning of your Sequence

9.4.2. Translate DNA

9.4.3. Tuning of Search Software Parameters

9.4.4. Statistics Analysis of Hits

9.4.5. Mapping Result Data

9.4.6. Analysis of Target Sequences

9.5.1. Database Sub-Libraries

9.5.2. Sequence Sets in BLAST searching

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

9.5.4. Multiple Sequence Files (MSF)

9.5.5. Lists within the Wisconsin Package Interface (SeqLab)

9.5.6. Impact of Electronic Networks, Time Effects and Location

9.5.7. Creation of own Databases

10.1 Principle of Multiple Sequence Alignment

10.1.1. Prerequisites

10.1.2. Finding the Best

10.1.3. Grouping

10.1.4. Result Evaluation

10.1.5. Limitations

10.2.1. Starting the Editor Mode

10.2.2. Coloring of Sequences

10.2.3. A small guided tour using SeqLab: Creation of a profile

10.3.1. Manual Start of an Alignment with the Multi-sequence Editor

10.3.2. Manual Editing of Sequence Alignments (text mode)

10.3.3. Manual Editing of File of Sequence Names

10.3.4. Automatic Creation of File of Sequence Names

10.3.5. Automatic Generation of a Multiple Sequence Alignment

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

10.3.7. Textual Presentation of the Alignment

10.3.8. Graphic Presentation of Similarity in the Alignment

10.3.9. Schematic Presentation Sequence Similarity

10.4.1. Creation of a Tree

10.4.2. PAUP-based Methods

10.6.1. Principle

10.6.2. Formats of Sequences

10.6.3. Profile Generation

10.6.4. Profile Searching

10.6.5. Profile Analysis

10.6.6. Profile scanning

11.1 History of This Document

11.1.1. Note on the Type of this Document

11.2.1. Conventions

11.2.2. Exercises

11.3.1. GCG CD Version

11.4.1. HTML Format

11.4.2. LATEX Format

11.4.3. Postscript Format

11.4.4. RTF Format

11.4.5. JAMF source code

11.5.1. Address

11.5.2. Configuration parameters

11.5.3. Configuration files

11.5.4. Prices

11.5.5. Acknowledgements

11.5.6. Known problems

11.6.1. Versions before 3.x

11.6.2. Version 3.0

11.6.3. Version 3.1

11.6.4. Version 3.2

11.6.5. Version information

12.1 Restrictions imposed by computer use

12.2.1. Operational security

12.2.2. Data protection

12.3.1. VMS

12.3.2. UNIX: ULTRIX

12.3.3. UNIX: OSF/1

12.3.4. UNIX: SunOs

12.3.5. UNIX: Solaris

12.3.6. UNIX: IRIX

12.3.7. Windows NT

12.4.1. Account

12.4.2. Equipment

12.4.3. Local Area Network

12.5.1. Local networks

12.5.2. Protocols

12.5.3. Internet

12.5.4. 'ftp', 'www', 'telnet'

12.5.5. 'HASSLE'

13.1 A

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

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