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Article #2539RE: [Bio-software] EvidentialGene : Evidence Directed Gene predictions for Eukaryotes
From: S.Prashant
Date: Tue, 18 Jan 2011 04:28
Date: Tue, 18 Jan 2011 04:28
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5641 bytes
Azzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz -----Original Message----- From: Don Gilbert Sent: 17.01.2011, 11:04 PM To: bio-soft@magpie.bio.indiana.edu Cc: Subject: [Bio-software] EvidentialGene : Evidence Directed Gene predictions for Eukaryotes Dear genomicists and genome informaticians, I've been working on practical use of gene prediction/annotation methods for arthropods for over 6 years now, and gotten to the point where this recipe works well, and can be generally useful for eukaryote genome annotations: EvidentialGene : Evidence Directed Gene predictions for Eukaryotes See http://arthropods.eugenes.org/genes2/ This is similar to others' genome annotation protocols, but differs in some of the gory details. In particular, it is designed for parallel genome analyses on computer grids and clusters, it handles the large volumes of RNA-seq data now being churned out (sort of, still working to improve aspects), and it has a specially designed "Best Evidential Gene" picking algorithm included as a last step in combining/filtering gene prediction sets. This is not yet a pipeline package, not something that others can run as a black box, where you feed in data and it spits out shiny new annotated gene sets. But it is a recipe with detailed steps that work for the eukaryotes I've tested it on. A few colleagues have given this recipe a beginning try; with some effort it appears that others can use this. So far we have applied it to Daphnia pulex and Daphnia magna, Pea aphid, Nasonia jewel wasp, and Theobroma cacao (the chocolate tree, where this worked well). Just now there is one fully worked public example at above URL, for Pea aphid. Final gene models for aphid are still in progress, from lots of new rna-seq evidence. The documentation is in a rough state. This document has gory details for pea_aphid annotations, http://arthropods.eugenes.org/genes2/pea_aphid2/docs/ aphid-genes-details.txt This will perhaps be of most use now to those of you who already are doing informatics of genome annotations, and know some of these methods. There may be parts of this you can incorporate or learn from. If you have interests in this, feel free to contact me. Don Gilbert, gilbertd at indiana edu -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ _______________________________________________ Bio-soft mailing list Bio-soft@net.bio.net http://www.bio.net/biomail/listinfo/bio-soft
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X-Google-Thread: fa6b6,8c6a5a4835045137,start X-Google-NewGroupId: yes X-Google-Attributes: gid6710630482,domainid0,public,usenet X-Google-Language: ENGLISH,ASCII-7-bit Path: arc1-ca.pugleaf.net!g2news1.google.com!news1.google.com!npeer01.iad.highwinds-media.com!news.highwinds-media.com!feed-me.highwinds-media.com!border3.nntp.dca.giganews.com!Xl.tags.giganews.com!border1.nntp.dca.giganews.com!nntp.giganews.com!local2.nntp.dca.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Mon, 17 Jan 2011 22:53:26 -0600 X-Envelope-From: prashantsingam@gmail.com DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:message-id:date:from:subject:to:reply-to :mime-version:x-priority:content-type:content-transfer-encoding; bh=PiSyPxmdffxFqNRW3aobVGAJzjgBSOmLstgogWC/Bp0=; b=I2XvDJkzxGA/WlmpGHddY+EUj+T/kLa0Ek3C1SasWX8jmGYi+g+S/G61u2p7AMI3w6 o+LnQwB31UWPhecNRLquYHh33Mum4/Mwf1VC2v7ze3wq5O+EWeFojRMOeKSV3M94wVAI m1SlYpRQeawq4r3Kiw8OAagd7YwVeAZaB9DVo= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=message-id:date:from:subject:to:reply-to:mime-version:x-priority :content-type:content-transfer-encoding; b=tBq3RsA+EPGZ7rdOTfTeIlp+whpoLfODdHLFdZQwX2ZFF6OUapPuAWGf5S8l/dbaGl QW3ghm+ip5FHKT9za6W/oobVS0SX5xBflXqCc4U79IBfxeQUGVwWzPkABuCORnn1Udd7 jmFYtWemDYXzJS2Og3GjqhVmfYKHTPyIe/lFI= Date: Tue, 18 Jan 2011 04:28:43 +0000 From: "S.Prashant" <prashantsingam@gmail.com> To: "bio-soft@magpie.bio.indiana.edu" <bio-soft@magpie.bio.indiana.edu>, "Don Gilbert" <gilbertd@oat.bio.indiana.edu> MIME-Version: 1.0 X-Priority: 3 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by net.bio.net id p0I4TNp00813 X-Mailman-Approved-At: Mon, 17 Jan 2011 23:52:47 -0500 X-BeenThere: bio-soft@net.bio.net X-Mailman-Version: 2.1.4 Precedence: list Reply-To: prashantsingam@gmail.com Organization: BIOSCI/IUBio, Biology Dept., Indiana University subject: RE: [Bio-software] EvidentialGene : Evidence Directed Gene predictions for Eukaryotes Newsgroups: bionet.software Message-ID: <mailman.709.1295326369.15153.bio-soft@net.bio.net> Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> X-Auth: PGPMoose V1.1 PGP bionet.software iQCVAwUBTTUcoqCIqsWvyF5FAQEK3gP/f3EI6pZLS/mcI7Hg++dqr151SCiPEIoS igvA+H3KTU+zLZGMTZPXbzT0gJa2Zlcd7P0dF3yMOYTOX/0f2HzOv83uWKSfhysS e8VX4SUmOwF1OeaFn042eaV8rOZowy37N4jshMuLNa4rmn2DMQ0GsjRZZzvO11AM sJHqx80KzV4= =REL/ Lines: 67 X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-zwE43EoHRcLWqo3Qs0mmSl68aYlWKpyovQ2px48Bu5/LCLcWnKbvVwdWvqooiaPFUwp54eoVOxO1ghF!zQPnPRtsM7byNmN0MKhZT7kzktMlmmmxhpDR081w9r8vJmATevM2bj5Y3QKMfHLAZxgNMuLjwMMe!EeO8FA== X-Complaints-To: abuse@giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40 X-Original-Bytes: 5232