Question: GPU-blast -> write PSI-blast yourself [help me understand the algoritm]
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gravatar for Xylanaser
17 months ago by
Xylanaser60
Poland - Warsaw - SGGW/WULS
Xylanaser60 wrote:

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

ADD COMMENTlink modified 17 months ago • written 17 months ago by Xylanaser60

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 REPLYlink written 17 months ago by lieven.sterck7.2k
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