[BiO BB] Fungal genefinding hints needed

[Mike Marchywka]

Do you have a link to some training/testing sets? I think one was mentioned for the
hmmer discussed by the original poster but wasn't sure what resources there are in
this area. Are there examples of known cases that are particularly confusing?

Thanks.



Mike Marchywka
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> Date: Mon, 17 Mar 2008 14:59:55 -0700
> From: sariego9 at yahoo.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Fungal genefinding hints needed
>
> 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" 
> 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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