Databases in the WWW

Elisabeth Gasteiger, July 2001
Useful starting points:ExPASy server http://www.expasy.org and its mirror sites:
http://ca.expasy.org, http://kr.expasy.org, http://au.expasy.org, http://tw.expasy.org
SWISS-PROT: [www|kr|ca|au|tw].expasy.org/sprot/
Amos’ WWW links: [www|kr|ca|au|tw].expasy.org/alinks.html
BioHunt: [www|kr|ca|au|tw].expasy.org/BioHunt/

General remark: SWISS-PROT is highly cross-referenced, so make use of these cross-references to get from SWISS-PROT to corresponding entries in other databases!

I)

  1. Look for the amino acid sequence of human carbonic anhydrase 2 in SWISS-PROT.
  2. Retrieve the corresponding nucleic acid sequence entries from the EMBL and GenBank databases. (Why are there more than one?)
  3. Look at a PDB file. (Why are there more than one?)
  4. Find the chromosomal location of human carbonic anhydrase 2
    • via MIM (Mendelian Inheritance inMan)
    • via GDB (Genome Data Base)
  5. Is carbonic anhydrase known for maize and drosophila? (possible approaches: SWISS-PROT/TrEMBL or EMBL or the genomic databases MaizeDb/Flybase (as the gene might be known but not sequenced))

II)

  1. Search for the SWISS-PROT entry corresponding to the yeast gene RPL36B.
  2. Follow the link to SGD (Saccharomyces Genome Database) to see the chromosomal location.
  3. Retrieve the SGD entry corresponding to the gene that is the second next gene in direction 5′ on the same strand of the chromosome.
  4. Follow the link to the YPD database.
  5. Find the subcellular location of the protein.
  6. Follow the link to SWISS-PROT.
  7. Have a look at the domain structure in the PRODOM database and retrieve a list of proteins sharing at least one domain with this protein.

III)

  1. Find a database of CFTR mutations (CFTR is the gene for cystic fibrosis) in the Web

IV)

  1. Find the ‘teashirt’ gene in FlyBase
  2. Retrieve, via FlyBase, the corresponding SWISS-PROT, EMBL and TRANSFAC (transcription factor db) entries.

V)

  1. Go to the ‘Genome Net’ server in Japan
  2. Look for a database called “KEGG”
  3. In KEGG, search for the enzyme with the EC (Enzyme classification) number EC 1.2.3.4
  4. Retrieve – the ENZYME entry (on ExPASy) via KEGG
    • the SWISS-PROT entry OXO1_HORVU via ENZYME
    • the corresponding PROSITE entry via SWISS-PROT