Faster version of RPS-BLAST (Reverse PSI-BLAST) USearch/Vsearch

Question

[thomasvangurp]

I am using NCBI's RPS-blast for finding conserved domains in protein sequence data. Given that usearch/vsearch/diamond are orders of magnitude faster than NCBI's blast (although with somewhat lower accuracy), I was wondering if anyone knows if a faster implementation of RPS-blast exists.

With kind regards, Thomas

Answer 1

[h.mon]

You can try UProC, but this tools has seen very few usage, so it would be advisable to benchmark it with a few hundred proteins from your dataset and check it against RPS-Blast and HMMER+Pfam.