Biocomputing

Gibson Group

EMBL

October 28th and 29th 1997

by Toby Gibson, Chenna Ramu and Christine Gemünd

The course consists of two introductory lectures on sequence analysis and two practicals introducing some of the tools available at EMBL on UNIX computers, or available through the WWW interface. Schedules for the practicals are provided on Web pages accessible by clicking on the links below.

In the practicals, the students will investigate some protein families as an introduction to sequence analysis tools available at EMBL on UNIX and the WWW. These will include SRS, Blast 2, Bioccellerator, GCG, Clustal X. The students will be split into two divisions and will probably have to be in groups of three per computer.

28 th October

• 9-10 am Lecture: Sequence Analysis at EMBL.
• Followed by Practical:
  • Division A. Practical 1: Sensitive DB searches on the WWW. SRS, Blast 2, Bic and Bic profiles.
  • Division B. Practical 2: Sequence Extraction, Alignment and Trees. Use of SRS. Clustal X, GCG package.

29 th October

• 9-10 am Lecture: Vertebrate polyploidy and other recent results from analysis of sequences.
• Followed by Practical:
  • Division A. Practical 2: Sequence Extraction, Alignment and Trees. Use of SRS. Clustal X, GCG package.
  • Division B. Practical 1. Sensitive DB searches on the WWW. SRS, Blast 2, Bic and Bic profiles.

Go to the student list to see which group you are in.

Practical 1

This practical introduces some web servers provided at EMBL. These can be accessed from any computer and are simple to use. Web servers are often the nicest way to do sequence analysis. But you should be aware that they can be unreliable, need constant care from their providers and are not suited to every task. Sometimes you have to run programs on local machines too.

• Part 1, SRS sequence extraction, Blast 2 and Bic_sw searches
• Part 2, Bic profile searching

Practical 2

This practical uses SRS on the WWW but the main focus is on X-Windows applications run on UNIX computers. At EMBL, it is especially important to be able to use GCG on UNIX. It offers many aspects of sequence analysis that are not available, or unsuited to WWW servers.

• Part 1, SRS sequence extraction, Clustal X alignment and tree, NJplot tree display on UNIX
• Part 2, GCG Package. Motifs, Dotplot comparison on UNIX

You can find this page at http://www.embl-heidelberg.de/~seqanal/courses/predoc97/Top.html