From bryanlepore at mail.utexas.edu Sun Feb 26 15:09:34 2006 From: bryanlepore at mail.utexas.edu (Bryan W. Lepore) Date: Sun Feb 26 15:09:46 2006 Subject: [Discuss] stamp and nucleic acid Message-ID: i'd like to extend a stamp alignment out to nucleic acids. googling gets lots of false positives e.g. protein alignment, nucleic acid alignment, maybe on the same webpage, but not both operating in parallel. so hasn't this been done or does any Barton group software offer this potential? -bryan From tom at compbio.dundee.ac.uk Mon Feb 27 10:54:13 2006 From: tom at compbio.dundee.ac.uk (Tom Walsh) Date: Mon Feb 27 10:54:19 2006 Subject: [Discuss] stamp and nucleic acid Message-ID: <4402DA55.8090102@compbio.dundee.ac.uk> Bryan W. Lepore wrote: >i'd like to extend a stamp alignment out to nucleic acids. googling gets lots >of false positives e.g. protein alignment, nucleic acid alignment, maybe on the >same webpage, but not both operating in parallel. > >so hasn't this been done or does any Barton group software offer this potential? > > STAMP works only on protein chains. It's not designed to fit structures in general (i.e. protein chains plus associated ligands). Is this what you trying to do? We don't have a program that does this. Tom -- Tom Walsh tom@compbio.dundee.ac.uk Tel.: +44 1382 348725 School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, UK ICQ 248982639 From geoff at compbio.dundee.ac.uk Mon Feb 27 10:57:17 2006 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Mon Feb 27 10:57:19 2006 Subject: [Discuss] stamp and nucleic acid In-Reply-To: <4402DA55.8090102@compbio.dundee.ac.uk> References: <4402DA55.8090102@compbio.dundee.ac.uk> Message-ID: Bryan, Rob Russell did extend STAMP to read and fit DNA/RNA for a study of the ribosome RNA structure, but I am not sure if this is in the currently distributed version. We will have to check. Geoff. On Mon, 27 Feb 2006, Tom Walsh wrote: > Bryan W. Lepore wrote: > >> i'd like to extend a stamp alignment out to nucleic acids. googling gets >> lots >> of false positives e.g. protein alignment, nucleic acid alignment, maybe on >> the >> same webpage, but not both operating in parallel. >> >> so hasn't this been done or does any Barton group software offer this >> potential? >> > STAMP works only on protein chains. It's not designed to fit structures > in general (i.e. protein chains plus associated ligands). Is this what you > trying to do? We don't have a program that does this. > > Tom > > > > > > -- > Tom Walsh tom@compbio.dundee.ac.uk Tel.: +44 1382 348725 > School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, UK ICQ > 248982639 > > _______________________________________________ > Discuss mailing list > Discuss@compbio.dundee.ac.uk > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk From bryanlepore at mail.utexas.edu Mon Feb 27 16:00:46 2006 From: bryanlepore at mail.utexas.edu (Bryan W. Lepore) Date: Mon Feb 27 16:01:02 2006 Subject: [Discuss] stamp and nucleic acid In-Reply-To: References: <4402DA55.8090102@compbio.dundee.ac.uk> Message-ID: On Mon, 27 Feb 2006, Geoff Barton wrote: > Rob Russell did extend STAMP to read and fit DNA/RNA for a study of the > ribosome RNA structure, that is interesting to know. my admittedly vague question is more along the lines of "can we take a structural alignment of protein _sequences_ a la STAMP->ALSCRIPT, the add the corresponding nucleic acids (mRNA exons, DNA, etc.) in there "somehow"... to see the whole pathway from gene to _protein_ structure. it seems this must have "been done already". -bryan From geoff at compbio.dundee.ac.uk Mon Feb 27 16:16:29 2006 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Mon Feb 27 16:16:42 2006 Subject: [Discuss] stamp and nucleic acid In-Reply-To: References: <4402DA55.8090102@compbio.dundee.ac.uk> Message-ID: Bryan, Sorry, that is a different question. You mean you have a protein sequence alignment to which you wish to add the corresponding DNA alignment. I'm afraid there is nothing from my group that does this at the moment, though it would be nice in some circumstances to do this. It would be possible to render something like this with ALSCRIPT, but it would be fiddly. Geoff. On Mon, 27 Feb 2006, Bryan W. Lepore wrote: > On Mon, 27 Feb 2006, Geoff Barton wrote: >> Rob Russell did extend STAMP to read and fit DNA/RNA for a study of the >> ribosome RNA structure, > > that is interesting to know. > > my admittedly vague question is more along the lines of "can we take a > structural alignment of protein _sequences_ a la STAMP->ALSCRIPT, the add the > corresponding nucleic acids (mRNA exons, DNA, etc.) in there "somehow"... to see > the whole pathway from gene to _protein_ structure. it seems this must have > "been done already". > > -bryan > _______________________________________________ > Discuss mailing list > Discuss@compbio.dundee.ac.uk > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk