The Sequence Databases: PRACTICAL

Navigating through Sequence Databases using SRS

  1. http to SRS at the EBI (http://srs.ebi.ac.uk:5000).
  2. start a new SRS session
  3. Top Page
    1. Browse available DataBanks
    2. Select SWISSPROT and EMBL
    3. click on Continue
  4. Query Form. Discuss fields
  5. Search for the word "actin" in AllText.
    55021 entries returned (1998-05-31). Some not related to Actin.
  6. Restrict search to Description field.
    7659 entries found.
  7. Restrict search to Phylogenetic groups. Search "eukaryota" in Organism
    2263 entries found
  8. Further restrict to more specific phylogenetic group
    TOTAL 7649
    EUKARYOTA 6678
    CHORDATA 5646
    MAMMALIA 5464
    PRIMATES 3415
    HUMAN 3413
  9. Restrict search within beta. Search "actin & beta" in Description and "eukaryota" in Organism
    872 entries found.
  10. View all entries in one single page.
  11. View with different views.
  12. Browse through the entries
    1. click on SWISSPROT:ACTB_HUMAN
    2. browse entry
    3. click on EC, MEDLINE, EMBL, PROSITE links.
  13. Define a new view that allows to correlate more easily DNA with protein sequences
    1. click on View Manager
    2. click on create
    3. select EMBL in first list and SWISSPROT in second list. give a name to the view. click on continue.
    4. select print whole entry in EMBL and SWISSPROT
    5. click on Top Page
    6. Select EMBL
    7. click on Continue
    8. Search "actin & beta" in Description and "eukaryota" in Organism
      855 entries found (we are only searching embl, now)
    9. View 500 in one page. Scrolling down the list of entries, we realize most of them are ESTs
    10. click on Query Form
    11. Search "actin & beta" in Description, "eukaryota" in Organism, and "dna" in Molecule
      34 entries found.
    12. View with newly created view. We can see clearly wich DNA sequences correspond to which amino acid sequences.
  14. 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.

  1. http to http://genome.imb-jena.de
  2. clik on Sequencing Projects: Human, cromosome 11.
  3. scroll down the list of single projects to (for instance) clone name LLNCO2N7 (not a very large contig)
  4. click on map
  5. click on analysis results
  6. browse and discuss results of automatic analysis.