worm base genes biomaRt filter

Question

[hamarillo]

Does anyone know what's the difference between:

• wormbase gene
• wormbase locus
• wormbase sequence name

I am using biomaRt to download all the C elegans genes, and between the possible filters are

with_wormbase_gene (WormBase Gene Accession) with_wormbase_locus (Wormbase locus ID(s)) with_wormbase_gseqname (WormBase Gene Sequence-name Accession)

[BruceB]

I assume you are using biomaRt to download from Ensembl, in which case you will be accessing data from WormBase release WS250. The current WormBase release is WS254, and can be accessed through the WormBase ParaSite BioMart (http://parasite.wormbase.org/biomart/martview).

Answer 1

[harold.smith.tarheel]

Gene = unique identifier in WormBase (format is 'WBGene' followed by 8-digit number, e.g., WBGene00006604)

Locus = genetically identified name (e.g., tra-1), or sequence name (for genes based solely on sequence)

Sequence name = cosmid/YAC identifier from the genome sequencing project (e.g., Y47D3A.6)