[BiO BB] Fungal genefinding hints needed

[Diego Martinez]

Hello Mark,

you might also try softberry.com, they make the popular fgenes and fgenesh programs, and I believe they have a 
web interface.  also, genewise in the wise2 package might be helpful, you can get to that (and download) at ebi.
also, augustus http://augustus.gobics.de/ has been popular lately, but I have not tried it personally.  I think in EMBOSS there is a dna - protein translator,
you can use that.  
I can go on about the genefinders if needed.  we used to use many different ones, and then choose the best for each locus using a filtering scheme.

Diego


----- Original Message ----
From: "mmiller at mail.usp.edu" <mmiller at mail.usp.edu>
To: bbb at bioinformatics.org
Sent: Saturday, March 15, 2008 11:30:36 AM
Subject: [BiO BB] Fungal genefinding hints needed


Hello, BBB.

A am trying to annotate a recently completed fungal genome.  I have been able to train GLimmerHMM against Aspergillus, scan my genome and generate a list of exons.  But that's the extent of my experience so far.

? Are the other genefinders I should be trying?  I had trouble compiling GeneZilla.
? Are there existing programs that can use a genomic FASTA file and  Glimmer coordinates to write out protein sequences in FASTA format?  Or do people in my position usually write their own script?
? Are there good on-line discussion groups for this sort of topic? 

Thanks,
Mark
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