Not sure if I understand the question right, but wouldn't phi-blast do trick. You supply on too your conserved pattern and blast again.
Christian Am 20.12.2017 19:37 schrieb "Keller, Jacob" <[email protected]>: > 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 > > > > +++++++++++++++++++++++++++++++++++++++++++++++++ > > Jacob Pearson Keller > > Research Scientist / Looger Lab > > HHMI Janelia Research Campus > > 19700 Helix Dr, Ashburn, VA 20147 > <https://maps.google.com/?q=19700+Helix+Dr,+Ashburn,+VA+20147&entry=gmail&source=g> > > (571)209-4000 x3159 <(571)%20209-4000> > > +++++++++++++++++++++++++++++++++++++++++++++++++ > > > > The content of this email is confidential and intended for the recipient > specified in message only. It is strictly forbidden to share any part of > this message with any third party, without a written consent of the sender. > If you received this message by mistake, please reply to this message and > follow with its deletion, so that we can ensure such a mistake does not > occur in the future. > > >
