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
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