[Bioperl-l] Re: bacterial genome annotation

[Marcus Claesson]

I now think there's another solution that blasting against the new
sequence. After I sent out my question I found a public program that
seem to solve the problem at least for prokaryotes. It's Sequin at
http://www.ncbi.nlm.nih.gov/Sequin/

It has quite a nice feature that checks the differences between old
and new sequence, let you scroll thorugh them and then updates. The
input is fasta format and a tab-separated textfile with annotations.
Sequin then creates a genbank entry that can be updated with new
sequence in fasta format.

To me this looks very good! Have a look at it!

Marcus


On Tue, 2003-07-15 at 15:35, Neil Saunders wrote:
> > 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