What about Dennis Madsen et al's "Indonesia"? http://xray.bmc.uu.se/dennis/
I don't think it's been updated in years (or I have a old link), but it's still quite nice as it runs locally using java. AGS > Date: Tue, 4 Mar 2008 12:02:20 -0800 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] multiple sequence alignment from multiple pairwise > structural alignments > To: CCP4BB@JISCMAIL.AC.UK > > On Tuesday 04 March 2008 11:13, Stephen Graham 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. > > My preference is for the CE-MC server. There are several sites that > offer this, or you can install it locally. Here's one: > bioinformatics.albany.edu/~cemc > > Another one is Tcoffee: > http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi > > When I've done head-to-head comparisons, I have found the output from > CE-MC to be preferable. In particular, in cases where you have two > structures A and B that have the same length but have an area in which > the structures differ, CE-MC will favor the alignment > AAAAAAaaa...AAAA > BBBBBB...bbbBBBB > whereas Tcoffee will report > AAAAAAaaaAAAA > BBBBBBbbbBBBB > > For my purposes, the first is correct, even if aaa and bbb are > sequence-homologous. > > > -- > Ethan A Merritt Courier Deliveries: 1959 NE Pacific > Dept of Biochemistry > Health Sciences Building > University of Washington - Seattle WA 98195-7742 _________________________________________________________________ Need to know the score, the latest news, or you need your Hotmail®-get your "fix". http://www.msnmobilefix.com/Default.aspx
