Entering edit mode
5.5 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
- I give fasta sequence as query
- blast build profile from alignment
- blast uses profile to search similarity in db (i dont know how it works for now)
- if theres another iteration blast uses alignment from lasst query as new query?
- build a profile from adding to last profile the new alignment new profile?
best, X
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.