European Molecular
Biology Computing Network - Biocomputing Tutorials DNA

DNA Sequence Analysis - Introduction

DNA Analysis tutorial contents:

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

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

NB 2: For the purposes of this tutorial, the GCG & EGCG packages will be jointly referred to as E/GCG.

This tutorial is divided into twelve parts:

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

Throughout, you will find links to:

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

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 ...

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.

Table of Contents Now you are ready for Part 1 - UNIX Basics   UNIX Basics

Already familiar with UNIX?

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

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

Good luck, Bonne chance, Held og lykke, viel Glück, Sucess, ...;

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!

SRS, Blast, Fasta Linkage ACeDB GDB v6 EMBnet Biocomputing Tutorials Internet for Biologists CRI-MAP DNA Sequence Analysis On-line Mendelian  
Inheritance in Man


Comments? Questions? Accolades? Comments? Questions? Accolades?
Please send them to David Featherston Please   ( )
Updated on Wednesday, 20 November, 1996
Copyright © 1995-1996 by David W. Featherston