Re: [ccp4bb] How to align a sequence to a know profile
I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Hi Yuan, You can use UCSF Chimera's Multalign Viewer tool to do this. Just open your alignment with that tool and use the "Edit->Add Sequence" menu item to add your sequence to the alignment. UCSF Chimera: http://www.cgl.ucsf.edu/chimera/ Multalign Viewer tool: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html specifically the "Add Sequence" part: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] How to align a sequence to a know profile
3-d coffee and expresso will align sequences without structures with sequences that do have structures in a structure-based sequence alignment: http://www.tcoffee.org/Projects_home_page/expresso_home_page.html perhaps this is along the lines of what Yuan is looking for? __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 1 Jun 2010, Thomas Juettemann wrote: Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of known structures and a sequence he wants to add to it. I am always keen to learn about alignment programs, it would be great to know how to use chainsaw for this problem. On Tue, Jun 1, 2010 at 02:20, Eleanor Dodson wrote: chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
Re: [ccp4bb] How to align a sequence to a know profile
Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of known structures and a sequence he wants to add to it. I am always keen to learn about alignment programs, it would be great to know how to use chainsaw for this problem. On Tue, Jun 1, 2010 at 02:20, Eleanor Dodson wrote: > chainsaw does just that > > eleanor > > 商元 wrote: >> >> Hello, everyone, >> I've a protein sequence of known domain. Based on structure alignment, >> I've got a alignment of those with known structures. Then how to add my >> sequence to the alignment?Any suggestions? >> Regards, >> Yuan SHANG >> >
Re: [ccp4bb] How to align a sequence to a know profile
chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
Re: [ccp4bb] How to align a sequence to a know profile
Dear Yuan, the MUSCLE program can do that for you. It is capable of doing profile-profile and profile-sequence alignments. http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497021 Section 2.10 of the manual should be what you want. Cheers, Thomas On Mon, May 31, 2010 at 01:46, Tim Gruene wrote: > Dear Yuan SHANG, > > you can use Jalview do create and edit an alignment with your sequence. > Jalview is available at http://www.jalview.org/, and I quite liked it when I > worked with it. > > Tim > > > On Mon, May 31, 2010 at 04:29:48PM +0800, 商元 wrote: >> Hello, everyone, >> I've a protein sequence of known domain. Based on structure alignment, >> I've got a alignment of those with known structures. Then how to add my >> sequence to the alignment?Any suggestions? >> Regards, >> Yuan SHANG > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.9 (GNU/Linux) > > iD8DBQFMA3djUxlJ7aRr7hoRArVqAJsGxH8tcPIzwtzpeGFSB7yNGWLBNACg3wbj > 5hpD2QWQG6h3X6ySCViGxDc= > =0qUC > -END PGP SIGNATURE- > >
Re: [ccp4bb] How to align a sequence to a know profile
Dear Yuan SHANG, you can use Jalview do create and edit an alignment with your sequence. Jalview is available at http://www.jalview.org/, and I quite liked it when I worked with it. Tim On Mon, May 31, 2010 at 04:29:48PM +0800, 商元 wrote: > Hello, everyone, > I've a protein sequence of known domain. Based on structure alignment, > I've got a alignment of those with known structures. Then how to add my > sequence to the alignment?Any suggestions? >Regards, > Yuan SHANG -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] How to align a sequence to a know profile
Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
