Question: Efficiently create PSI-BLAST-like PSSMs from very large MSAs
gravatar for alquraishi
3.6 years ago by
alquraishi0 wrote:

I have a multiple sequence alignment that I'd like to turn into a PSI-BLAST-like PSSM. I'm aware of this solution, but unfortunately PSI-BLAST appears to croak on very large alignments (hundreds of thousands of sequences). Are there other tools out there that generate the same PSI-BLAST style PSSM files that can handle very large MSAs?

blast alignment pssm • 1.7k views
ADD COMMENTlink written 3.6 years ago by alquraishi0

We had success in leveraging PSI-BLAST for generating PSSMs for a large number of sequences (See database of PSSM profiles here; publication here). Can you give the specifics of the issues?

ADD REPLYlink written 3.6 years ago by Khader Shameer18k

I have an MSA that has about 200,000 sequences. I ran PSI-BLAST for over 12 hours and it did not finish (on this single MSA). Has your experience been different?

ADD REPLYlink written 3.6 years ago by alquraishi0
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