Re: [ccp4bb] Structure based and motif based sequence alignment
This was one of the things that Indonesia was written for (a long time ago, in a galaxy far, far away), although I'm not sure if it will still run. If you're desperate, see http://xray.bmc.uu.se/~dennis/ --Gerard On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] Structure based and motif based sequence alignment
We did something like this with esprit. You get the sequence alignments from Psiblast or whatever you fancy, then edit in the structural alignment into the txt file it generates. Messy but successful.. Eleanor On 12/01/2010 03:44 PM, Gerard DVD Kleywegt wrote: This was one of the things that Indonesia was written for (a long time ago, in a galaxy far, far away), although I'm not sure if it will still run. If you're desperate, see http://xray.bmc.uu.se/~dennis/ --Gerard On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
[ccp4bb] Structure based and motif based sequence alignment
Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir
Re: [ccp4bb] Structure based and motif based sequence alignment
Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir Hi there, Ages ago, for this type of work (fine-tuning sequence alignments), I was loading pre-aligned (or not pre-aligned) sequences and was editing the alignment by hand using a sequence alignment editor. This editor was working on VAX/VMS systems, which no-one uses anymore (I haven't touched VMS in many many years). So I had a look at what sequence alignment editors are available today using google, and I came across this: Jalview (http://www.jalview.org ). Unfortunately, it seems it does not wish to install on my Linux box so I don't know if the software does what you want it to do. And it is not clear to me exactly what you mean by extending the sequence only at the c-terminus. Fred.
Re: [ccp4bb] Structure based and motif based sequence alignment
Dear Fred; Thanks for the reply! extending at the c-terminus means that this protein only N-terminus structure has been solved and I want to include the residues as well in the sequence alignment which are not in the structure. Regards; Bashir On Fri, November 26, 2010 13:38, Vellieux Frederic wrote: Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir Hi there, Ages ago, for this type of work (fine-tuning sequence alignments), I was loading pre-aligned (or not pre-aligned) sequences and was editing the alignment by hand using a sequence alignment editor. This editor was working on VAX/VMS systems, which no-one uses anymore (I haven't touched VMS in many many years). So I had a look at what sequence alignment editors are available today using google, and I came across this: Jalview (http://www.jalview.org ). Unfortunately, it seems it does not wish to install on my Linux box so I don't know if the software does what you want it to do. And it is not clear to me exactly what you mean by extending the sequence only at the c-terminus. Fred. -- Muhammad Bashir Khan ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
Re: [ccp4bb] Structure based and motif based sequence alignment
Hi Bashir, You can use Pipealign http://bips.u-strasbg.fr/PipeAlign/ it will do for you all the steps from the sequence search (one sequence as a query) to the multiple alignement of the complete sequence. It should be able to manage sequences of different length and the structure based alignement should be ok (The Rascal step should do this job). good luck claudine Le 26/11/2010 15:19, Muhammed bashir Khan a écrit : Dear Fred; Thanks for the reply! extending at the c-terminus means that this protein only N-terminus structure has been solved and I want to include the residues as well in the sequence alignment which are not in the structure. Regards; Bashir On Fri, November 26, 2010 13:38, Vellieux Frederic wrote: Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. Remember the structure are known only for the two proteins. Any suggestion will be highly appreciated! Regards and have a nice weekend. Bashir Hi there, Ages ago, for this type of work (fine-tuning sequence alignments), I was loading pre-aligned (or not pre-aligned) sequences and was editing the alignment by hand using a sequence alignment editor. This editor was working on VAX/VMS systems, which no-one uses anymore (I haven't touched VMS in many many years). So I had a look at what sequence alignment editors are available today using google, and I came across this: Jalview (http://www.jalview.org ). Unfortunately, it seems it does not wish to install on my Linux box so I don't know if the software does what you want it to do. And it is not clear to me exactly what you mean by extending the sequence only at the c-terminus. Fred. -- Pr Claudine MAYER Université Paris Diderot - Paris 7 Dynamique structurale des Macromolécules Département de Biologie Structurale et Chimie Institut Pasteur 25 rue du Dr Roux 75 015 PARIS Tel. 01 45 68 83 87 Mobil. 06 07 23 51 16 Fax. 01 45 68 89 93 Mail. ma...@pasteur.fr
Re: [ccp4bb] Structure based and motif based sequence alignment
Hello Bashir, If I understand your question correctly, Expresso and 3D-Coffee from the T-coffee people will do just what you want. They align sequences while utilizing any available structural information. http://www.tcoffee.org/Projects_home_page/expresso_home_page.html hope that is what you are looking for, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: | Dear All; | | I have structures of two protein one full-length while the other truncated | at the c-terminus(one from prokaryote while the other from eukaryotes). | Now I want to do the sequence alignment of these two proteins from all | species in such a way that the structure based sequence remain constant | while extending the sequence only at the c-terminus. Remember the | structure are known only for the two proteins. | | Any suggestion will be highly appreciated! | | Regards and have a nice weekend. | | Bashir |
Re: [ccp4bb] Structure based and motif based sequence alignment
I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. IIUC : profile 1 = *structure-based* sequence alignment i.e. from STAMP (THESEUS?) profile 2 = a huge sequence alignment i.e. from MAFFT or CLUSTALW2 with both *profiles* in hand, these comes to mind : [1] clustalx : load profile 1. choose profile mode (?) then add profile 2 to it [2] Jalview : load profile 1. then add profile 2 to it [3] mafft : command line : mafft-profile profile_1.aln profile_2.aln all.aln there's pulldowns in [1,2] that will lead the way. i can say [1,2] work in my hands to align sequences, and then browse through them or print them. haven't tried [3] for structure-based profile alignment. ... BTW, if anyone wants a molecular replacement search probe, this is very interesting : phenix.sculptor a_structure.pdb huge_sequence_alignment.[ali,fasta,..] BTW they are helpful over on the Jalview discussion group : http://www.jalview.org/mailman/listinfo/jalview-discuss HTH -Bryan
