[Bioperl-l] Re: bacterial genome annotation

Neil Saunders neil.saunders at unsw.edu.au
Wed Jul 16 01:35:32 EDT 2003

> 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.

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


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