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BMCBI
2010

Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

10 years 4 months ago
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors
Background: Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. Results: We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. Conclusions: This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid i...
Karel Zimmermann, Jean-François Gibrat
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Karel Zimmermann, Jean-François Gibrat
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