[BiO BB] Extracting upstream sequence of a gene

[kannaiah at bsd.uchicago.edu]

Hi Paulo,

I didnt really see a way to do multiple search on the genome browser.
To extract from a certain region, i guess then i will have to compile the start
and end regions of the gene in the chromosomes before hand?

-Kiran

Quoting Paulo Nuin <pnuin at terra.com.br>:

> 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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