From midori at ebi.ac.uk Fri Feb 1 22:00:05 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 2 Feb 2008 06:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802020600.m1260661239806@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080202/05723f65/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080202/05723f65/attachment.pl From midori at ebi.ac.uk Sat Feb 2 22:00:05 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sun, 3 Feb 2008 06:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802030600.m13605U1391788@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080203/a6637e55/attachment.pl From val at sanger.ac.uk Mon Feb 4 08:56:13 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Mon, 04 Feb 2008 16:56:13 +0000 Subject: [annotation] gamma-aminobutyric acid metabolic process/derivatives question Message-ID: <47A743AD.3070308@sanger.ac.uk> I have a gene uga1 annotated to 4-aminobutyrate transaminase activity and gamma-aminobutyric acid metabolic process at the moment in GO derivatives-of-x metabolism under x metabolism generally so gamma-aminobutyric acid metabolic process inherits process annotations to fatty acid metabolic process and amine metabolic process http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0009448 even though GABA isn't a 'fatty acid' Do people have any feelings whether this is correct for GO ? i.e. would you expect to see genes annotated to "gamma-aminobutyric acid metabolic process" annotated to "fatty acid metabolic process" ? respond to SF https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1885151&group_id=36855 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From midori at ebi.ac.uk Mon Feb 4 22:00:08 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 5 Feb 2008 06:00:08 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802050600.m15608f1209325@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080205/e092d91e/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080205/e092d91e/attachment.pl From midori at ebi.ac.uk Tue Feb 5 22:00:08 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 6 Feb 2008 06:00:08 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802060600.m16608o1374733@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080209/524b7112/attachment.pl From midori at ebi.ac.uk Mon Feb 11 22:00:07 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 12 Feb 2008 06:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802120600.m1C60781332104@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080212/d0383554/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080212/d0383554/attachment.pl From midori at ebi.ac.uk Tue Feb 12 22:00:07 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 13 Feb 2008 06:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802130600.m1D607R1080823@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080213/4b69b885/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080213/4b69b885/attachment.pl From midori at ebi.ac.uk Wed Feb 13 22:00:09 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 14 Feb 2008 06:00:09 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802140600.m1E609T1404841@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080214/409e5e4a/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080214/409e5e4a/attachment.pl From midori at ebi.ac.uk Thu Feb 14 22:00:07 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 15 Feb 2008 06:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802150600.m1F608v1289719@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080215/0db7ae9e/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080215/0db7ae9e/attachment.pl From midori at ebi.ac.uk Fri Feb 15 22:00:06 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 16 Feb 2008 06:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802160600.m1G606J1557916@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080216/c261add0/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080216/c261add0/attachment.pl From midori at ebi.ac.uk Mon Feb 18 22:00:06 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 19 Feb 2008 06:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802190600.m1J60651231097@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080219/389bb32b/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080221/f19b30c5/attachment.pl From midori at ebi.ac.uk Fri Feb 22 22:00:08 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 23 Feb 2008 06:00:08 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802230600.m1N609x1345661@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080223/b1323a27/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080223/b1323a27/attachment.pl From midori at ebi.ac.uk Tue Feb 26 22:00:06 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 27 Feb 2008 06:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200802270600.m1R606t1278474@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080227/fe20c12b/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080227/fe20c12b/attachment.pl From val at sanger.ac.uk Wed Feb 27 03:26:09 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 27 Feb 2008 11:26:09 +0000 Subject: [annotation] a question about ribosomes Message-ID: <47C548D1.2070800@sanger.ac.uk> As part of a collaboration we are looking in some at detail at some aspects of ribosome biology. I am trying to find a clear 'structural map' of the eukaryotic ribosome which shows the postion of the individual subunits. Something like this: http://www.genome.jp/kegg/pathway/map/map03010.gif but where is is easier to discriminate the position of the specific subunit in the 3D structure. Does anybody know of anything off the top of their head? Thanks Val -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From hjd at informatics.jax.org Thu Feb 28 10:20:42 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 28 Feb 2008 13:20:42 -0500 Subject: [annotation] a question about ribosomes In-Reply-To: <47C548D1.2070800@sanger.ac.uk> References: <47C548D1.2070800@sanger.ac.uk> Message-ID: <47C6FB7A.5000209@informatics.jax.org> Valerie Wood wrote: > > As part of a collaboration we are looking in some at detail at some > aspects of ribosome biology. I am trying to find a clear 'structural > map' of the eukaryotic ribosome which shows the postion of the > individual subunits. > > Something like this: > > http://www.genome.jp/kegg/pathway/map/map03010.gif > > but where is is easier to discriminate the position of the specific > subunit in the 3D structure. > > Does anybody know of anything off the top of their head? > > Thanks > > Val > > > > > > > I have forwarded this to a ribsome guru at MIT From val at sanger.ac.uk Fri Feb 29 02:57:59 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 29 Feb 2008 10:57:59 +0000 Subject: [annotation] a question about ribosomes In-Reply-To: <47C6FB7A.5000209@informatics.jax.org> References: <47C548D1.2070800@sanger.ac.uk> <47C6FB7A.5000209@informatics.jax.org> Message-ID: <47C7E537.5090008@sanger.ac.uk> Thanks Harold, I had a good paper suggested by Peter D'E (PMID: 11701127) and Sue Rhee suggested PDB (which I could probably use but I had trouble identifying a model of an entire eukaryotic ribosome using the search). If they have any good suggestions though please forward them as I won't be working on this for a week or so. Thanks everyone. Val Harold Drabkin wrote: > Valerie Wood wrote: > >> >> As part of a collaboration we are looking in some at detail at some >> aspects of ribosome biology. I am trying to find a clear 'structural >> map' of the eukaryotic ribosome which shows the postion of the >> individual subunits. >> >> Something like this: >> >> http://www.genome.jp/kegg/pathway/map/map03010.gif >> >> but where is is easier to discriminate the position of the specific >> subunit in the 3D structure. >> >> Does anybody know of anything off the top of their head? >> >> Thanks >> >> Val >> >> >> >> >> >> >> I have forwarded this to a ribsome guru at MIT > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.