[Biopython] Pulling Alignment From PSI-Blast Output

[Brett Bowman]

I'm trying to use the PSI-Blast results from a series of proteins to detect
distant homologues, using HMMs of various sorts.  Currently I'm pulling down
the sequence IDs with PSI-Blast, downloading the full sequences from NCBI,
then aligning everything with ClustalW or Muscle.  However this is eating up
way more processor time than I have to spare, so I want to just pull the
full multi-sequence alignment from the PSI-blast results if possible (OUTFMT
option #3 or 4), for use in building the HMMs.  But it doesn't look like
AlignIO has a module for reading the peculiar format that PSI-Blast
generates...

Has this been done before, or will I need to write my own parser?

Brett Bowman
Woelk Lab
UCSD School of Medicine