[BiO BB] Fungal genefinding hints needed

Michael Muratet mmuratet at hudsonalpha.org
Mon Mar 17 16:48:00 EDT 2008


How about TwinScan? It employs the concept of an 'informant' database  
which in this case would be C. neoformans  (as I recall).

Good luck


On Mar 15, 2008, at 12:30 PM, <mmiller at mail.usp.edu> 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
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