[BiO BB] Extracting upstream sequence of a gene

[Paulo Nuin]

Hi

If you have the IDs of these genes you can do that on the UCSC genome 
browser. You can set a region to download automatically from a multiple 
search.

Regards

Paulo


kannaiah at bsd.uchicago.edu wrote:
> Hello,
>
> I have seen a few posts asking similar questions. I am looking to do something
> similar too. 
>
> I want to extract the upstream sequence of genes (upto 3000bp upstream) in
> Human. But going thru the ensembl website is ok, if one has few genes.
>
> But i have a few hundred genes. I was wondering what would be the best way to
> automate this.
> Should i try blasting the gene sequences to the Human Chromosome files, and then
> parse the blast output to get the position of the genes, and go back and read
> the chromosome sequence where it was found and get the upstream sequence.
>
> That would be a long way, hopefully there is someother shorter way to do this,
> which i am not aware of.
> Any suggestions would be welcome:)
>
> Thank you
>
> -hak
>
>
>
>
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