Exonerate and GFF3 for GBrowse??
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Exonerate and GFF3 for GBrowse??
by Bob Freeman-2
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Does anyone know how to go from Exonerate output to GFF3? Currently, it only outputs GFF2.
I thought I read that importing GFF2 into Chado is not a good idea, esp. when trying to represent ESTs and mRNAs (cDNAs) aligned against scaffolds. So, I'm hunting around for a way to convert my Exonerate EST/mRNAs alignments to GFF3 for importing into Chado. Or am I going about this bass-ackwards? TIA, Bob ----------------------------------------------------- Bob Freeman, Ph.D. Acorn Worm Informatics, Kirschner lab Dept of Systems Biology, Alpert 524 Harvard Medical School 200 Longwood Avenue Boston, MA 02115 617/432.2293, vox The only other person I've apologized to is my mother and that was court ordered. ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Exonerate and GFF3 for GBrowse??
by Bob Freeman-2
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Thanks, Don. You're a life saver. All the links pointing to Jason's
old script are dead. Either that, or I haven't search far enough. -b On Nov 9, 2009, at 5:38 PM, Don Gilbert wrote: > > Bob, > > Jason Stajich wrote a useful process_exonerate_gff3 perl; I've a > variant of that > I use, here: > http://eugenes.org/gmod/genogrid/scripts/process_exonerate_gff3.perl > which avoids use of bioperl and is somewhat faster. > > - Don Gilbert > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd@...--http://marmot.bio.indiana.edu/ ----------------------------------------------------- Bob Freeman, Ph.D. Acorn Worm Informatics, Kirschner lab Dept of Systems Biology, Alpert 524 Harvard Medical School 200 Longwood Avenue Boston, MA 02115 617/432.2293, vox The only other person I've apologized to is my mother and that was court ordered. -- Karen Walker from Will & Grace ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Exonerate and GFF3 for GBrowse??
by Jason Stajich-3
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sorry bob - I am guessing don's will work fine. some things are
defunct when my former inst stopped supporting some of my websites. trying to migrate important things to git when I am reminded they are misising - this folder has some variants of that script in there including a + and - bioperl one. http://github.com/hyphaltip/genome-scripts/tree/master/data_format/ -jason On Nov 9, 2009, at 3:45 PM, Bob Freeman wrote: > Thanks, Don. You're a life saver. All the links pointing to Jason's > old script are dead. Either that, or I haven't search far enough. > > -b > > On Nov 9, 2009, at 5:38 PM, Don Gilbert wrote: > >> >> Bob, >> >> Jason Stajich wrote a useful process_exonerate_gff3 perl; I've a >> variant of that >> I use, here: >> http://eugenes.org/gmod/genogrid/scripts/process_exonerate_gff3.perl >> which avoids use of bioperl and is somewhat faster. >> >> - Don Gilbert >> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 >> -- gilbertd@...--http://marmot.bio.indiana.edu/ > > ----------------------------------------------------- > Bob Freeman, Ph.D. > Acorn Worm Informatics, Kirschner lab > Dept of Systems Biology, Alpert 524 > Harvard Medical School > 200 Longwood Avenue > Boston, MA 02115 > 617/432.2293, vox > > The only other person I've apologized to is my mother and that was > court ordered. > -- Karen Walker from Will & Grace > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Jason Stajich jason.stajich@... jason@... ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Exonerate and GFF3 for GBrowse??
by Bob Freeman-2
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Thanks, Jason. I didn't want to bug you until I needed it ... getting the Exonerate data in has been on the back burner for some time.
In any case, I'll download this as well. Congrats, btw, on the faculty job! Best, Bob On Nov 11, 2009, at 2:43 AM, Jason Stajich wrote: sorry bob - I am guessing don's will work fine. some things are defunct when my former inst stopped supporting some of my websites. trying to migrate important things to git when I am reminded they are misising - this folder has some variants of that script in there including a + and - bioperl one. http://github.com/hyphaltip/genome-scripts/tree/master/data_format/ -jason On Nov 9, 2009, at 3:45 PM, Bob Freeman wrote: Thanks, Don. You're a life saver. All the links pointing to Jason's old script are dead. Either that, or I haven't search far enough. -b On Nov 9, 2009, at 5:38 PM, Don Gilbert wrote: Bob, Jason Stajich wrote a useful process_exonerate_gff3 perl; I've a variant of that I use, here: http://eugenes.org/gmod/genogrid/scripts/process_exonerate_gff3.perl which avoids use of bioperl and is somewhat faster. - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@...--http://marmot.bio.indiana.edu/ ----------------------------------------------------- Bob Freeman, Ph.D. Acorn Worm Informatics, Kirschner lab Dept of Systems Biology, Alpert 524 Harvard Medical School 200 Longwood Avenue Boston, MA 02115 617/432.2293, vox The only other person I've apologized to is my mother and that was court ordered. ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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