Amino Acid Relationships (long)

David Jones jones at bsmsol1.ucl.ac.uk
Thu Dec 17 16:26:46 EST 1992

As a follow-up to Harry Mangalam's summary of methods  for representing amino
acid  similarities,  people  might also be  interested in  the following  two
references (one in press, one in print):

The first  paper is something  of a sequel to  Willie Taylor's original  Venn
diagram paper from 1986...

Taylor, W.R., Jones, D.T.
"Deriving an Amino Acid Distance Matrix."
J. Theor. Biol. in press. (1993)


Various methods were investigated  to convert an amino acid similarity matrix
into a low-dimensional, metric distance matrix.  Using projection techniques,
no  unique  transformation  was   found  and  of  the  many  inversion  forms
investigated, simple negation normalised by the diagonal  elements produced a
good fit to the original data. An  inter-row distance also gave a  comparable
fit and  when evaluated by weighted  least-squares minimisation  was found to
be  preferable. A  rank-ordered form  of  the matrices  was also  derived  by
constraining  neighbours to  be  equidistant in  (3)  space. This  produced a
network configuration  not unlike  that produced  in a  previous analysis  of
amino  acid  physico-chemical  properties.  The  derived   forms  might  find
applications in  sequence alignment,  including pattern matching  algorithms,
and the construction of phylogenetic trees.

The other reference is...

Taylor, W.R.
"A template based method of pattern matching in protein sequences."
Prog. Biophys. Mol. Biol. 54:159-252 (1989) (published in 1991).

This paper  contains possibly the oldest  reference in  any molecular biology
paper: Wan,  "The I  Ching", privately published  (1142 BC).  If you want  to
know  what Gray codes,  the I  Ching, and  the genetic  code have to  do with
representing amino acid similarities, then this is the paper for you!

David Jones
Biomolecular Structure and Modelling Unit
University College London

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