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how do I automatically update gene coordinates after re-sequencing

Kevin Karplus karplus at bray.cse.ucsc.edu
Tue Jul 15 18:04:40 EST 2003

In article <e818c15b.0307100224.2e6ef92a at posting.google.com>, 
Marcus Claesson wrote:
> I'm faced with a problem that I'm sure many others are having as well.
> We are annotating a bacterial genome and as a first step we pick out
> gene coordinates and possible functions by doing blast searches of the
> genome against various databases. The quality of our sequence is
> increased after some following resequencing, so the gene coordinates
> needs to be updated.
> One could do this by writing a program that blastn all the genes
> against the new sequence and then pick out the new coordinates for the
> nearly identical hits. Gene duplicates etc could make it a bit messy
> though.
> Has anyone out there done this before, and do you have any tips?
> Would be extremely grateful if you could share them!

The genome browser people do this all the time on the human, mouse,
and rat genomes.  Try contacting them at genome at soe.ucsc.edu

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.

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