[BiO BB] Fungal genefinding hints needed

Martin Gollery marty.gollery at gmail.com
Mon Mar 17 17:06:10 EDT 2008

Hi Mark,

Take a look at the Fungal HMM database (FPfam) which was written up
last year in BMC genomics.


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. intikhab.alam at manchester.ac.uk

On Sat, Mar 15, 2008 at 10:30 AM,  <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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Martin Gollery
Senior Bioinformatics Scientist
TimeLogic- a Division of Active Motif
880 Northwood Blvd. Suite 7
Incline Village, NV 89451

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