I am also not sure of what your goal is, but you can build a sequence profile for your sequence and use that profile as input instead of your sequence. You can do this by aligning a set of sequences homologous to your target sequence, and use that alignment as input for, for example, HMMER or HHPred. You can also let HMMER or HHPred build these profiles for you by giving your sequence as input and play with the parameters.

Best,

Dr. Joana Pereira
--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Spemannstraße 35
72076 Tübingen
GERMANY

On 20 Dec 2017, at 18:35, Keller, Jacob <[log in to unmask]> wrote:

Dear Crystallographer-Bioinformaticians,
 
Is anyone aware of a way to tweak BLAST or similar software to be able to specify certain residues to be absolutely required, e.g., active site residues? I guess one can winnow broad-scale resuts with scripts, but it would seem to be a pretty common type of thing to do, and might change results slightly a la psi-BLAST.
 
All the best,
 
Jacob Keller
 
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Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
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