Practical Courses on Basic Sequence Analysis
November 13th-15th, 2000
by Toby Gibson, Chenna Ramu, Christine Gemünd and José Castresana
The courses consist of four 1/2 day modules that you can take individually or together.
A short introduction will be followed by use of sequence analysis programs using typical sequence examples. The course covers the most common tasks in sequence analysis including database search and retrieval, multiple sequence alignment and sequence trees. With the human and other eukaryotic genomes becoming available, we have added some gene analysis tools that we did not cover in previous years. If you are comfortable with these core tasks, it should not be difficult to find out how to do other analyses in the future.
In the practicals, you will investigate some protein families and gene sequences as an introduction to sequence analysis tools available at EMBL on UNIX and the WWW. These will include SRS, Blast 2, Bioccelerator, SMART, GCG, Clustal X, Gene2EST, Artemis and tree display programs. The students will be split into two groups and will be paired up for each X-terminal. Practicals will take place in the computer teaching lab, room V124/V125.
Monday 13th November
Tuesday 14th November
Wednesday 15th November
Course 1. Web Tools (SRS, Blast2, Bioccelerator, SMART)
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. Database search tools are well-suited to web servers and we will try out the Blast and Bioccelerator servers at EMBL.
Course 2. Using the GCG Sequence Analysis Package on UNIX
At EMBL, it is especially important to be able to use the GCG package on UNIX. It offers many aspects of sequence analysis that are not available on, or are unsuited 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.
Course 3. Exploring gene sequences with Artemis and Gene2EST
Artemis is a genome sequence display and annotation program from the Sanger Centre. It uses EMBL format sequence files and displays the features listed in the feature table. These features can be edited - Artemis is used to annotate newly sequenced "small" genomes (bacteria and so forth) at the Sanger centre. It is very useful for anyone who has to work with large DNA segments encoding complex genetic information. Gene2EST is a new server developed by our group for querying EST databases with large (gene-sized) queries. In favourable cases (=lots of ESTs) Gene2EST can efficiently reveal spliced gene structure and whether there are alternatively spliced products. Artemis is used to display the graphical output of Gene2EST.
Course 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/Nov00/Top.html