[BioC] from BAC name to list of genes in that BAC

[Cui, Wenwu (NIH/NLM/NCBI) [C]]

Giving you knew clone RP11-238E12 in ChrX, a straightforward alternative might be to parse: 

http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=X&maps=genes,clone[RP11-238E12]-r&cmd=txt

You can modify Build version as well.

Good luck!

Wenwu Cui, PhD

-----Original Message-----
From: Hilmar Berger [mailto:hilmar.berger at imise.uni-leipzig.de] 
Sent: Friday, January 19, 2007 7:23 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] from BAC name to list of genes in that BAC

Hi Federico,

Federico Abascal schrieb:

> CTD-2082H4   
> CTD-2060E7   
> RP11-130N6   
> RP11-142M16   
> RP11-221G13   
> RP11-238E12   

OK, these are standard BAC-Names you might find in public databases.

> 
>>Anyway, usually you should be able to get a table of BAC clones and 
>>other parameters (genomic location, (uni)gene id etc.) which might help 
>>in identifiying the genes in question.
 >
> yes, I have that information.
> Isn't there a way in Bioconductor to ask for the genes present between
> nucleotides 130000 and 145000??

Last time I had to map BAC clones to genes (actually to probesets) I 
chose to use a list from GoldenPath (http://genome.ucsc.edu) because 
that way it is easier to chose the release version of the genome 
assembly. This release (or approximate date) should match the one that 
was used for creation of your BAC-annotation list, since different 
releases might have different positions for your BACs and genes.
The table "knownGene" from GoldenPath gives you start and end positions 
for each gene. A simple filter in R (e.g. "subset(gene.list, 
gene.chrom=BAC.chrom & gene.start >= BAC.start & gene.stop <= BAC.stop", 
done for every BAC)  should be sufficient to get all genes within or 
nearby your BAC-clones.

Regards,
Hilmar



-- 

Hilmar Berger
Studienkoordinator
Institut für medizinische Informatik, Statistik und Epidemiologie
Universität Leipzig
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D-04107 Leipzig

Tel. +49 341 97 16 101
Fax. +49 341 97 16 109
email: hilmar.berger at imise.uni-leipzig.de

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