[BioC] Genbank accessions for GOstuff

[Sean Davis]

On 8/9/06 3:02 AM, "adlai burman" <fsajb4 at uaf.edu> wrote:

> The GO packages seem to rely solely on LocusLink ids but there are a
> host of onboard affy translators. Now LL seems to be deprecated and I
> don't use affymetrix.

Locuslink has simply been replaced by Entrez Gene.  For nearly all intents
and purposes, Locuslink still exists, but has the name Entrez Gene.  So,
when you read about Locuslink-based analyses, these are still appropriate
and possible.  

> I have thousands of genes which I would love to
> continue using with BioC. Does anyone know of a mapping somewhere where
> I can batch convert gb nums or gene symbols in a way that R's GO
> packages will accept. Thanks in advance.

The AnnBuilder package is the way to build an annotation package for your
genes.  It takes genbank ids and makes an annotation package for your array
that you can then use for downstream analyses.

Alternatively, there are several online resources that allow you to do GO
analyses using genbank IDs.  For example, the DAVID/EASE system
(http://david.niaid.nih.gov/david) supports genbank IDs as input.

Finally, there are tools to convert your genbank accessions to more useable
IDs, like Entrez Gene (Locuslink) IDs.  For example, Stanford Source (
http://source.stanford.edu/cgi-bin/source/sourceSearch) can convert between
genbank IDs and multiple gene identifiers.

Sean