I'm attempting to generate an rpsblast database from a set of protein cluster alignments. For most of them, I could use blastpgp -B <alignment> to generate the PSSM without problem, but several of the alignments (namely the large ones, or the ones with huge sequences) crash (seg-fault) blastpgp (legacy v2.2.23, if it matters).
However, these alignments can be hmmbuilt into HMMER profiles without complaint. I know there has to be a way to convert the HMMs to psiblast profiles, since does it for CDD with PFAM and TIGRFAM. I'm just hoping it something better than exporting the alignment, then blastpgp -- particularly since that's what's crashing.
Anyone got a script to convert them directly?