Hi, "Indonesia" is great for this.
http://xray.bmc.uu.se/dennis/ Cheers, Martin On Jan 25, 2011, at 10:50 PM, Katherine Sippel wrote: > Hi all, > > I was wondering if you know of a program that can do protein sequence > alignments around experimentally determined equivalent residues (i.e. > biochemists have determined via mutagenesis and kinetics that residues 3,6 > and 9 of protein X are the equivalent of residues 7, 14, 21 in homologous > protein Y). I've got a good sized pool of homologous sequences to improved > the accuracy of the alignments and a few of the homologs have pdbs. I get > close in T-coffee, but it is missing a few theoretically conserved residues > and it is an unwieldy job for manual correction. Any assistance would be > appreciated. > > Thanks, > > Katherine
