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: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: [email protected] 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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
