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
