how do I automatically update gene coordinates after re-sequencing

Marcus Claesson m.claesson at student.ucc.ie
Thu Jul 10 20:53:20 EST 2003


Hi,

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!

Best regards,
Marcus




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