how do I automatically update gene coordinates after re-sequencing the genome

Gordon D. Pusch gdpusch at NO.xnet.SPAM.com
Mon Jul 14 11:49:46 EST 2003


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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