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 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only [EMAIL PROTECTED] Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on [EMAIL PROTECTED] if no reply here. Thanks. > Date: Mon, 17 Mar 2008 14:59:55 -0700 > From: [EMAIL PROTECTED] > To: [email protected] > 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: "[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 _________________________________________________________________ Windows Live Hotmail is giving away Zunes. http://www.windowslive-hotmail.com/ZuneADay/?locale=en-US&ocid=TXT_TAGLM_Mobile_Zune_V3 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
