[Bioperl-l] Re: bacterial genome annotation

[Neil Saunders]

> One could do this by writing a perl script 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.

Using blastn for annotation is an extremely messy solution.  It's very
unlikely that you will identify complete genes this way - they would
need to be almost identical and the starts/stops would have to align.

You should use an ORF finding package such as Critica or Glimmer.  I
believe there are Bioperl modules to deal with Glimmer output too.  Mail
me if you need more help with this.

Neil
-- 
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php