[Biopython] Multiple Sequence Alignment Conversion: A2M and A3M from Fasta

[Brett Bowman]

I'm writing a Biopython script to pipeline the following process:
1) Parse Fasta From File
2) Blast it against NCBI and pull down a range of solid hits
3) Align the sequence with Muscle or ClustalW
4) Build a HMM profile of the alignment with HHmake

1-3 I've got down pat, its step 4 that seems to be the problem.
 In particular, HHmake appears to prefer A2M or A3M format alignments,
and produces inferior results when fed an Aligned Fasta (*.AFA).  Both
alignment programs output to Fasta or ClustalW, but not A2M or A3M, and in
addition I can't seem to find a definition for either format online
anywhere.

So: Does anyone know if there is a way to convert to A2M or A3M
with Biopython?  They do not appear supported by AlignIO.  Otherwise, does
anyone know where I could find a definition for the formats online so that I
can write my own conversion?

Brett Bowman
Woelk Lab
UCSD Medical School