In the referenced article, george at immuno.esam.nwu.edu (George Johnson) writes:
>All in the Family...
>>We have had a couple of questions about our 'family' designation for the
>dump files and Postscript files. These families do not and are not meant
>to correspond to families cited in the literature. They are purely
>something generated at our end for the purpose of combining sequences of
>high AMINO ACID homology within the variable region together to help us
>and others locate sequences that seem to belong with each other more than
>with other sequences.
>>Each family is composed of sequences that differ from one another by 12
>amino acids or less. These amino acid differences do not take into
>consideration the codons that generated them. It is a division based on
>amino acid sequence only. (A glance over the codon sequences though
>indicates that the codons are quite similar too).
>Please keep in mind that the family designation is for our purposes and
>for purposes of locating similar sequences. There is no relationship
>between our families and everyone else's families that we know of.
I went through the Mouse VH and V kappa sequences last March
to put the new sequences into similar subgroups to those in
the 5th Edition Sequences of Proteins of Immunological Interest.
I made a bit of an effort to get it right, but its quite probably
wrong in places. I'd be interested to have any corrections.
This is how I ended up classifying the sequences:
5th Edition "Dump format family"
Subgroup
MH1A I, II
MH1B III, IV
MH2A V, VI, VIII, IX, X, XI
MH2B VII, XII, XIII
MH2C XV
MH3A XVI, XVII
MH3B XVIII, XXVI
MH3C XIX, XX, XXI
MH3D XXII, XXIII, XXV
MH5A XIV, XXIV
MKL1 I, II
MKL2 III, IV, V, VI, VII
MKL3 VIII, IX, X, XXVI
MKL4 XII
MKL5 XIII, XIV, XV, XVI, XVII, XVIII, XIX, XX, XXII, XXIII, XXIV,XXV
MKL6 XI
(Where MH2A is Mouse Heavy Chain Variable region IIa)
Andrew Henry
School of Biology and Biochemistry
University of Bath
Bath
Avon, BA2 7AY
Great Britain.
Tel (0225) 826826 ext 5411
Fax (0225) 826449
email A.H.Henry at bath.ac.uk
