[Biopython-dev] Kabat wire ( or wild goose ) chase

Cayte katel at worldpath.net
Sat May 19 02:43:58 EDT 2001

  I found that the subscripts of the Kabat numbers do not represent
alternatives.  A helpful email informed me that  more than likely the
letters flag insertions compared to a reference.  When I checked the PubMed
reference for a Kabat output file, I found that the sequence in the NCBI
nucleotide database matched the Kabat residues chained together,without any
special handling of the subscripted residues.  My guess is that the
reference used is the canonical form, sort of a template for what a plain
vanilla antibody should contain.

SEQTPA        109   100 gat ASP D
SEQTPA        110  100A cta LEU L
SEQTPA        111  100B ccg PRO P
SEQTPA        112  100C cac HIS H
SEQTPA        113  100D aat ASN N
SEQTPA        114  100E gat ASP D
SEQTPA        115  100F ggt GLY G
SEQTPA        116  100G --- --- -
SEQTPA        117  100H --- --- -
SEQTPA        118  100I --- --- -
SEQTPA        119  100J --- --- -
SEQTPA        120  100K ttt PHE F


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