[BiO BB] Extracting upstream sequence of a gene

[Mike Marchywka]

In my prior post, I discussed one reason that I may want to download
the entire genome and apply various translation schemes ( model
faulty ribosomes), pick out certain peptides, and then run them through
blast to see if they have been observed anywhere. 

Someone posted the ensemble link the other day: 
ftp://ftp.ensembl.org/pub/current_homo_sapiens/data/fasta/dna/
and, sure enough, if I gunzip it I have what I need- 
one chromosome at a time may even fit in memory.


Now, I just need some codon libraries.  I can find simple
things like this:
http://www.cbs.dtu.dk/courses/27613/codon.html

but are there species specific probabilities anywhere?
I did find this: 

http://www.cbs.dtu.dk/dtucourse/27611spring2006/Lecture03/virtualribosome.pdf

Thanks.


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Mike Marchywka
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-----Original Message-----
From:
bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati
cs.org]On Behalf Of kannaiah at bsd.uchicago.edu
Sent: MondayMay-08-2006 06:03 PM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] Extracting upstream sequence of a gene


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