Hi Stephen, Fun question! A quick google search with "structure based sequence alignment" gave me this site which looks promising:
http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html Let me know how it turns out! Sophia On Tue, Mar 4, 2008 at 11:13 AM, Stephen Graham <[EMAIL PROTECTED]> wrote: > Hi all, > > I would like to generate a structure-based multiple sequence alignment > using 4 structures. I have already generated pairwise alignments for > each 'pair' of structures (6 alignments in all). Is there a program > out there that can take a number of aligned structures (or even just a > number of pairwise sequence alignments) and calculate the 'best' > multiple sequence alignment? Please note that there is absolutely no > sequence conservation between these structures, making standard > sequence-based alignment tools pretty useless. > > Thanks, > > Stephen > > -- > Dr Stephen Graham > Nuffield Medical Fellow > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > Roosevelt Drive > Oxford OX3 7BN > United Kingdom > Phone: +44 1865 287 549 >
