Help:What can BioMart do for me

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You can use BioMart to perform bulk data retrieval from VectorBase. Most of the information you see on the genome browser can be queried and displayed/downloaded in a variety of formats.

Here are some examples of what you can do with VectorBase's BioMart:

[edit] Gene location and structure

  • Count the number of genes on chromosome 2L (Anopheles gambiae)
  • Download the cDNA sequences of all genes with annotated 5' and 3' UTRs and two or more transcripts
  • Get genes with non-synonymous coding SNPs

[edit] Gene function

  • Download the protein sequences of all GTPase activator proteins (GO:0005096)
  • Display the GO terms for all genes with reporters on the Anopheles/Plasmodium Affymetrix microarray
  • Display the InterPro domains assigned to genes which are associated with a list of coordinately expressed microarray reporters (e.g. Anopheles gambiae array EMBL_MMC1_20k_v1, reporters 4A3A-AAT-A-10 4A3B-AAG-E-03 4A3B-AAC-D-03 4A3B-AAH-D-09)

[edit] Multi-species comparisons

  • Get a list of Anopheles gambiae genes with orthologues in Aedes aegypti and the corresponding percent identities (from protein-protein alignments)
  • Find the Aedes aegypti genes represented on the ND TIGRTC microarray which have orthologues in Anopheles gambiae which are represented on the EMBL MMC1 array (this is an example of a BioMart query made on two databases/species simultaneously).

It is important to remember that nearly all of the restrictions (e.g. on chromosome 2L, with function GO:0005096) can be combined with "AND" to create more specific queries.

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