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.

I know that CSI-Blast can get a checkpoint via: https://github.com/cangermueller/csblast/blob/master/README_CSBLAST

csbuild -i infile.seq -o outfile.chk -D K4000.crf -O chk

But I don't know how to pipe this to the PSI-Blast, and to get the PSSM as the final output. (For each sequence).

Thanks!