I'm trying to get the PSSMs (i.e per=site probability of each AA) for a batch of protein sequences.
I haven't used PSI-BLAST or CS-BLAST in the past, and am unfamiliar with the exact commands needed to pipe them together, and to get the output.
I'd like to use CSI-BLAST on each sequence, then to run 2 PSI-Blast iterations according to that, then to get the profile/PSSM of each sequence as the output.
- But I don't know how to pipe this to the PSI-Blast, andto get the PSSM as the final output. (For each sequence).