BASIC PROTOCOL 4: EXAMINING A MOLECULAR SEQUENCE IN C. ELEGANS

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WormBase has Sequence Pages as well as Gene Pages. Sequence Pages are focused on details of the nucleotide and predicted protein-coding sequences of genes.

Necessary Resources

Hardware

   A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)

Software

   Web browser such as Internet Explorer (http://www.microsoft.com) or Firefox (http://www.mozilla.org/firefox)

1. From any page where a molecular sequence is given as relevant to some other object (such as zyg-1, which has the synonym F59E12.2; (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_03.png), click on the relevant Sequence Report or Sequence name link. This will lead to a Sequence page.

Fig_1_8_05.png

Like a Gene page, a Sequence will have diverse information, with a somewhat greater emphasis on genomic sequence rather than classical biology.

The F59E12.2 Sequence page in WS147 gives a schematic diagram of F59E12.2's organization in the genome somewhat different from that on the Gene page, a BLAST (UNIT 3.3) search launcher, external links of the protein sequence to GenPept and SwissProt, and precise numerical coordinates for the F59E12.2 transcription unit along with the identities of cDNAs matching it. The BLAST search is automatically set up against WormBase's genomic sequence data by clicking on the "Run BLAST or BLAT" button (see Basic Protocol 9). This Sequence page is also be a convenient place to get the sequence in FASTA format (Apweiler, 2005; Appendix 1B) for BLAST searches outside WormBase. Given the F59E12.2 Sequence page, one can cut and paste it in FASTA format directly into one of the search pages at the NCBI (http://www.ncbi.nlm.nih.gov/BLAST; UNITS 3.3 & 3.4) or into a more specialized server. The Sequence page also gives links to the Protein page for zyg-1/F59E12.2 and to the C. briggsae ortholog of zyg-1.

2. Click the "Click Here to Browse" link to display the corresponding region in the Genome Brower (see Basic Protocol 7).