Hi Mark, Take a look at the Fungal HMM database (FPfam) which was written up last year in BMC genomics.
Cheers, Marty A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. Alam I, Hubbard SJ, Oliver SG, Rattray M. School of Computer Science, University of Manchester, Kilburn Building, Manchester, UK. [EMAIL PROTECTED] On Sat, Mar 15, 2008 at 10:30 AM, <[EMAIL PROTECTED]> wrote: > > 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 > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
