m.claesson at student.ucc.ie (Marcus Claesson) writes:
> 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.
Use the NUCmer wrapper for the MUMmer whole-genome alignment program,
<http://www.tigr.org/software/mummer/>.
A brief discussion of NUCmer may be found in the MUMmer manual,
<http://www.tigr.org/software/mummer/manual/#alignment>,
and also in the paper describing MUMmer-2:
<http://www.tigr.org/software/mummer/MUMmer2.pdf>.
-- Gordon D. Pusch
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