[BiO BB] Extracting upstream sequence of a gene

[kannaiah at bsd.uchicago.edu]

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




-------------------------------------------------
This email is intended only for the use of the individual or entity to which
it is addressed and may contain information that is privileged and
confidential.  If the reader of this email message is not the intended
recipient, you are hereby notified that any dissemination, distribution, or
copying of this communication is prohibited.  If you have received this email
in error, please notify the sender and destroy/delete all copies of the
transmittal.  Thank you.
-------------------------------------------------