DNA Sequence Analysis - Introduction

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DNA Analysis tutorial contents:

UNIX Basics	Sequence Assembly 1	Sequence Assembly 2	Editing & Exchange	Sequence DataBases	Typical E/GCG Programmes
Sequence Comparison	Searching Databases 1	Multiple Alignment	Searching Databases 2	Other Programmes	HELP!
On-Line Manuals	Appendix A: GCG & EGCG Pgms	Appendix B: Staden Pgms	Appendix C: Hints & Answers	Bibliography & Links	Datasets

There are three popular sets of DNA and protein sequence analysis programmes available via most EMBnet nodes:

• The Staden Package, from Rodger Staden et al, MRC Cambridge, UK
   
• The Wisconsin Package (GCG), from the Genetics Computer Group, Inc. USA
   
• EGCG (Extended GCG), from a consortium of researchers mostly based in Europe at EMBnet Nodes

Exploring the complete range of programmes in each package is beyond the scope of this tutorial. Fortunately, the three packages have substantial overlap in the function of their programmes, so that learning in one package speeds use of another. We will consider representative or important programmes from each package, starting with how to manage a sequencing project in the Staden package. Later, as GCG and EGCG programmes are introduced, most of the main functional groupings of all packages will be covered.

NB 1: Complete listings of all programmes, organised by function, are given in the appendices:

Appendix A - GCG & EGCG
Appendix B - Staden

This tutorial is divided into twelve parts:

1. UNIX Basics
2. Sequence Fragment Assembly with Staden - 1
3. Sequence Fragment Assembly with Staden - 2
4. Sequence Editing and Exchange
5. Sequence Databases
6. Typical E/GCG Programmes
7. Sequence Comparison
8. Searching Databases - 1
9. Multiple Sequence Alignment
10. Searching Databases - 2
11. Other Programmes
12. Getting HELP!

Throughout, you will find links to:

• the Staden, GCG, & EGCG manuals (World Wide Web versions, where possible),
• the Table of Contents for the tutorial,
• Appendix A - A Quick List of E/GCG Programmes,
• Appendix B - A Quick List of Staden Programmes,
• Appendix C - Some Hints for the exercises,
• and other references.

For those of you without data, please get some from the

• example datasets page.

NB:

This is an INTERACTIVE tutorial; you will benefit most by FOLLOWING the instructions, through READING the examples, and DOING the exercises! Exercises are indicated by italics in nested paragraphs ...

Exercise X.y: ... like this!

For the majority of the exercises, you need to run an interactive login session with your EMBnet Node host computer while you read the tutorial with your web browser. Be certain your web browser is set-up to call a terminal emulation programme or xterm window in response to the telnet:// URL. If you need some help with these technical details, browse the HELP! page.

Please choose your EMBnet Node host from this list, and use the link back to the DNA Sequence Analysis tutorial to continue.
Follow your usual login procedure on the telnet window that will appear. Move this window to the right of your screen, so it "fits" between the up and down scroll bar arrows of your web browser, like this.

Part 1 - UNIX Basics  

Already familiar with UNIX?

Start with Part 2 - DNA Sequence Assembly with Staden - 1   (under construction!)

Instead, start with Part 4 - DNA Sequence Editing and Exchange  

Have some fun doing this tutorial, and PLEASE send your comments and questions!

If you are keen to have MORE information about the Staden Package, GCG, or EGCG,
check the Bibliography Page.  

Oh, and if this information came to you V E R Y   S L O W L Y, check the PING! page to find which of the EMBnet Web Server Nodes is "closest" to you!