The Sequence Databases: PRACTICAL
Navigating through Sequence Databases using SRS
- http to SRS at the EBI (http://srs.ebi.ac.uk:5000).
- start a new SRS session
- Top Page
- Browse available DataBanks
- Select SWISSPROT and EMBL
- click on Continue
- Query Form. Discuss fields
- Search for the word "actin" in AllText.
55021 entries returned (1998-05-31).
Some not related to Actin.
- Restrict search to Description field.
7659 entries found.
- Restrict search to Phylogenetic groups. Search "eukaryota" in Organism
2263 entries found
- Further restrict to more specific phylogenetic group
- Restrict search within beta. Search "actin & beta" in Description and "eukaryota" in Organism
872 entries found.
- View all entries in one single page.
- View with different views.
- Browse through the entries
- click on SWISSPROT:ACTB_HUMAN
- browse entry
- click on EC, MEDLINE, EMBL, PROSITE links.
- Define a new view that allows to correlate more easily DNA with protein sequences
- click on View Manager
- click on create
- select EMBL in first list and SWISSPROT in second list.
give a name to the view. click on continue.
- select print whole entry in EMBL and SWISSPROT
- click on Top Page
- Select EMBL
- click on Continue
- Search "actin & beta" in Description and "eukaryota" in Organism
855 entries found (we are only searching embl, now)
- View 500 in one page. Scrolling down the list of entries,
we realize most of them are ESTs
- click on Query Form
- Search "actin & beta" in Description, "eukaryota" in Organism, and "dna" in Molecule
34 entries found.
- View with newly created view. We can see clearly wich DNA sequences correspond to which amino acid sequences.
- click on Query Manager
Accessing the Data Generated at a Genome Center
We will visit the Genome Sequence Center in Jena (Germany), the second
Sequencing Center in Europe, after the Sanger Center.
- http to http://genome.imb-jena.de
- clik on Sequencing Projects: Human, cromosome 11.
- scroll down the list of single projects to (for instance) clone
name LLNCO2N7 (not a very large contig)
- click on map
- click on analysis results
- browse and discuss results of automatic analysis.