Page 3 of the goseq documentation states

"In order to link GO categories to genes, goseq uses the organism packages from Bioconductor.
These packages are named org.<Genome>.<ID>.db, where <Genome> is a short string identifying
the genome and <ID> is a short string identifying the gene identi_er. Currently, goseq will
automatically retrieve the mapping between GO categories and genes from the relevant package
(as long as it is installed) for commonly used genome/ID combinations."

Let's say I want to use the organism package for the Apis mellifera version 2 genome, a supported genome according to the goseq supportedGenomes() command.  I see that there are several packages that follow the naming convention org.<Genome>.<ID>.db, but none of these is for the Apis version 2 genome.  What organism package do I install for Apis mellifera 2?  Can I use BSgenome.Amellifera.UCSC.apiMel2 even though it does not follow the proper naming scheme?

Thanks.

Vanessa

Research Molecular Biologist
USDA-ARS
Carl Hayden Bee Research Center
2000 E. Allen Rd., Tucson, AZ  85719

(520) 647-9269

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