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 latest database and the Gene dataset.
• Within the Filter section;
  • In the Location section, enable the Chromosome filter, and set to C.elegans Chr 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 Phenotype section,
    
    • enable [Function] RNAi Phenotypes that are set to Scored for and observed, Only
  • enable [Function] RNAi phenotype and set to larval_lethal
  • In the Annotation section,
    
    • enable [Transcript] UTR annotation and set to UTR5+UTR3,

• Within the Attributes section,
  • Select Gene Sequences option,
  • In Sequence Type, select Peptides,
  • In Header Attributes, Molecular names, select WB WormPep ID.
  • Click the <Results> button to run the query.
    
  • The results are shown [HERE].

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