[BioC] from BAC name to list of genes in that BAC
Federico Abascal
fabascal at cnb.uam.es
Fri Jan 19 12:52:00 CET 2007
thank you very much for your responses Hilmar and Sean.
Hilmar Berger wrote:
> mapping BAC clones to genomic positions and genes can be a time
> consuming process, especially if you have to do it manually. If public
> databases can help you depends on the way the BAC clones are named.
> Could you give some example ?
>
Here are some examples. I was unable to obtain information from the UCSC
table browser (as Sean suggested), although I have to try it more.
CTD-2082H4
CTD-2060E7
RP11-130N6
RP11-142M16
RP11-221G13
RP11-238E12
CTD-2088A19
GS1-225F6
RP11-48J15
RP11-4D2
RP11-82L3
RP11-71M14
RP11-135H9
RP11-256K9
RP11-65G9
RP11-185N10
RP11-140H23
RP11-247J14
> 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??
Best,
Federico
>> Estimated colleagues,
>>
>> I am working with CGH data. I have the name of the BAC clones and their
>> chromosome locations. They correspond to OncoBAC arrays (?).
>> Is there any way in bioconductor to determine which genes belong to each
>> BAC clone?
>>
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