Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
POSA at the Godzik lab does exactly what you are after, flexibly! http://fatcat.burnham.org/POSA/ Hi all=A3=AC I want to produce structure-based multiple sequence alignment of my =20= protein with five of its homologs on DALI server. However, when I =20 tried the "Database Search Form", only one homolog was picked up =20 from PDB. If I align my protein with each homolog by the "DaliLite =20 Pairwise comparison", how can I combine them together? Thanks in advance. Best regards, =09 Sincerely, Dalei Wu Drug Discovery and Design Center Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 555 Zu Chongzhi Road, Shanghai, 201203, China [EMAIL PROTECTED] 2007-12-05
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
Christoph Gille's program STRAP generates structure-based multiple sequence alignment, which can be combined with sequences for which no structure is available. http://www.charite.de/bioinf/strap/ Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ - On 5 Dec 2007, at 05:03, david wu wrote: Hi all， I want to produce structure-based multiple sequence alignment of my protein with five of its homologs on DALI server. However, when I tried the "Database Search Form", only one homolog was picked up from PDB. If I align my protein with each homolog by the "DaliLite Pairwise comparison", how can I combine them together? Thanks in advance. Best regards, Sincerely, Dalei Wu Drug Discovery and Design Center Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 555 Zu Chongzhi Road, Shanghai, 201203, China [EMAIL PROTECTED] 2007-12-05
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
Hi, I would suggest the indonesia program... easy to use and very flexible. http://xray.bmc.uu.se/dennis/ Cheers Dave david wu wrote: > Hi all， > > I want to produce structure-based multiple sequence alignment of my protein > with five of its homologs on DALI server. However, when I tried the "Database > Search Form", only one homolog was picked up from PDB. If I align my protein > with each homolog by the "DaliLite Pairwise comparison", how can I combine > them together? > > Thanks in advance. > > > Best regards, > > Sincerely, > > Dalei Wu > Drug Discovery and Design Center > Shanghai Institute of Materia Medica > Shanghai Institutes for Biological Sciences > Chinese Academy of Sciences > 555 Zu Chongzhi Road, Shanghai, 201203, China > [EMAIL PROTECTED] > 2007-12-05
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
You can perform a multiple structural alignment using MUSTANG ( http://www.bx.psu.edu/arun/research/mustang/), which draws upon some of the underpinnings of the DALI approach. James
[ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
Hi all， I want to produce structure-based multiple sequence alignment of my protein with five of its homologs on DALI server. However, when I tried the "Database Search Form", only one homolog was picked up from PDB. If I align my protein with each homolog by the "DaliLite Pairwise comparison", how can I combine them together? Thanks in advance. Best regards, Sincerely, Dalei Wu Drug Discovery and Design Center Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 555 Zu Chongzhi Road, Shanghai, 201203, China [EMAIL PROTECTED] 2007-12-05
