Representing A2M format with BioXSD

From Rost Lab Open

The A2M format is used as a format for multiple alignments of protein or nucleic-acid sequences.

BioXSD is the proposed common exchange format for basic bioinformatics data.

Option1 Option2 - perhaps preferred
            gap                    gap
          +----+                  +---+
                     occurrence
       +------------------------------------+
SEQ1 _______________________________________________
  fea ... homology
  occ
    alignment
      REF ___ gap&ins

SEQ2  __________________________________________
  fea ... homology
  occ
    alignment
      REF ___ gap&ins
            gap                    gap
          +----+                  +---+
                     occurrence
       +------------------------------------+
REF _______________________________________________
  fea ... homology
  occ
    alignment
      SEQ1 ___ gap&ins

  occ
    alignment
      SEQ2 ___ gap&ins


REF is e.g. an HMM model. SEQ is e.g. an amino acid sequence.