Biocomputing
Gibson Group
EMBL
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EMBL Hamburg Outstation
Practical Course on Sequence Analysis
May 5th-6th, 1999
by Toby Gibson, Chenna Ramu, Christine Gemünd and Jose Castresana, EMBL, Heidelberg
The course consists of four half-day practicals introducing some of the tools available at the EMBL outstation on UNIX computers, or available at EMBL Heidelberg through the WWW interface. The course is based on one that we gave at EMBL last autumn. Schedules for the practicals are provided on Web pages accessible by clicking on the links below. Introductory lectures will be given for some of the practicals.
In the practicals, the students will investigate some protein families as an introduction to the various sequence analysis tools. These will include SRS, Blast 2, Bioccelerator, GCG, Clustal X and tree display programs. It is recommended that the students be paired up for each Workstation/ X-terminal, as this will encourage discussion of the problems thrown up during the practicals.
Thursday 5th May
Friday 6th May
Practical 1. Web Tools (SRS, Blast2, Bioccelerator)
This practical introduces some web servers provided at EMBL, Heidelberg. 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. Database search tools are well-suited to web servers and we will try out the Blast and Bioccelerator servers at EMBL.
Practical 2. Using the GCG Sequence Analysis Package on UNIX
It is a good idea to be able to use the GCG package on UNIX. It offers many aspects of sequence analysis that are not available on, or are unsuitable for WWW servers. We will do exercises involving one, two or many sequences. Once you have mastered the WPI X-windows interface and SEQLAB multiple sequence editor, you will be able to run many other applications without much difficulty.
Practical 3. Exploring sequence databases with SRS
SRS, the Sequence Retrieval System, is a powerful program for indexing and retrieving data from sequence databases. SRS was developed at EMBL and, more recently, has been maintained at the EBI. Keywords are used to retrieve information from databases in SRS but links between databases allows users to get much more information than the keyword alone could retrieve. The course covers the WWW interface only: SRS is not installed at hamburg, so the command line interface cannot be covered.
Practical 4. Generating trees from aligned sequences
Molecular Evolution has revolutionised phylogenetic analysis (although it can never replace Paleontology because there is no implicit measure of time). For bench scientists, it can also be useful to produce trees from multiple alignments, even when evolution is only indirectly relevant. For example, it is important to distinguish orthologues from paralogues when extrapolating gene function between organisms.
You can find this page at http://www.embl-heidelberg.de/~seqanal/courses/Hamburg5.99/Top.html