GPU-blast -> write PSI-blast yourself [help me understand the algoritm]
0
0
Entering edit mode
3.1 years ago
Xylanaser ▴ 80

Hey. I want to write a program that uses gpu-blast to make psi-blast several runs and give me the profile as output. Can you help me understand what's psi-blast algoritm do? I found some data about but have problem to understand it well.

please send me some articles or links about this or write me how this works

  1. I give fasta sequence as query
  2. blast build profile from alignment
  3. blast uses profile to search similarity in db (i dont know how it works for now)
  4. if theres another iteration blast uses alignment from lasst query as new query?
  5. build a profile from adding to last profile the new alignment new profile?

best, X

gpu-blast psi-blast protein algoritm blast • 884 views
ADD COMMENT
0
Entering edit mode

that's pretty much spot on how psi-blast works indeed. Except that in step 3 it initially uses the 'normal' blast and from then on adds sequences to the profile and scans again (repeat steps 4&5) .

The screening of the sequences with the profile is more a HMMer like search than a sequence based search.

ADD REPLY

Login before adding your answer.

Traffic: 1804 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6