[BioC] Mapping

[Sean Davis]

Juan,

The information for genbank to GO can be obtained by mapping in the
following way:

GenBank-->Unigene-->Locuslink-->GO

The genbank accession numbers for all unigene clusters are included in the
file Hs.data.gz at ftp.ncbi.nih.gov.  As for Gene Names, there are multiple
places to look for this information.  Ensembl has an open mysql server that
probably has a crossreference table of gene names to ensembl genes that
could then be used to access GO information.  Locuslink also has an alias
field that contains multiple different gene names for a given locuslink ID.
There are probably online tools to do both of these one-at-a-time, but to do
many (as in a whole array), you will probably have to code in perl.

In bioconductor, you can use AnnBuilder to do much of the work for you.
Look at the vignettes for that package which lets you build annotation
packages (which include GO mapping) based on genbank accessions, unigene,
locuslink, or IMAGE clone.

Sean

On 3/31/04 3:39 AM, "Juan Pablo Grassi" <JGrassi at seznam.cz> wrote:

> Hello.
> 
> I have a problem trying to get a mapping between differents Gene IDs and GO
> Ids.
> I have found function to get mappings between LocusLink Id and Unigene and GO
> ids.
> But now, I need mappings between GeneBank and GO ids, and GeneNames and GO
> ids.
> 
> Anybody know functions to do so ?
> 
> Thanks for any help.
> 
> 
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