Data mining:WormMart:Example 2

Example 2: From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, have an observed larval lethal phenotype in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence

• Start a new WormMart query and;
  • Select the Gene dataset.
  • Click <next> to proceed to the FILTER page.
• On the FILTER page;
  • In the Identification section, enable the Limit to Species filter, and set to Caenorhabditis elegans,
  • In the Location section, enable the Limit to Chromosome filter, and set to III,
  • In the Homologs/Orthologs section;
    • enable the Homologs in Species filter and set to Caenorhabditis briggsae,
    • enable the Homologs which share filter and set to Compara Ortholog, Only
  • In the Annotation section,
    
    • enable [Transcript] UTR annotation and set to UTR5+UTR3,
    • enable [Function] RNAi phenotype and set to LVL larval_lethal
    • enable [FUNCTION] RNAi Phenotypes that are set to Scored for and observed, Only
  • The above selection is shown [HERE].
  • Click next to proceed to the OUTPUT page.

• On the OUTPUT page,
  • In the Select the Attribute Page section, select Gene, CDS and Protein Sequences option,
  • In the SEQUENCES section, select Peptides,
  • In the Header Information, Molecular names section, select WB WormPep ID.
  • The above selection is shown [HERE].
  • Click export to run the query.
  • The results are shown [HERE].

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