Friday, December 14, 2012

1212.3205 (Olivier Rivoire)

Elements of Coevolution in Biological Sequences    [PDF]

Olivier Rivoire
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure, and sectors, which are larger groups of structurally connected amino acids that underly the biochemical properties of proteins. By reconciling two approaches for analyzing correlations in multiple sequence alignments, we uncover a new class of coevolving units, called 'sectons'. Sectons provide a conceptual link between coevolving contacts and sectors. The methods and results that we present are general, and relevant beyond protein structures. This generality is illustrated with an analysis of the co-occurrence of orthologous genes in bacterial genomes.
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