I am reading this paper on protein fold classification and am particularly interested in their formulation of the profile-based composition vector (PCV). I downloaded an arbitrary set of proteins from PDB, hoping that I could construct a PCV for one of the proteins in that set.
Given a query protein sequence
query.faa and a database of protein sequences
db.faa, how can I generate a PSI-BLAST profile for
query.faa? I have looked at the help statement for the
psiblast program distributed with NCBI BLAST+ 2.2.25, but I don't see any relevant options.