Evolutionary profiles from the QR factorization of multiple sequence ...
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by choosing representative protein structures that best preserve the phylogenetic tree .... best represent the evolutionary history of a group of .... Illustration of QH,.
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Evolutionary profiles from the QR factorization of multiple sequence alignments Anurag Sethi, Patrick O’Donoghue, and Zaida Luthey-Schulten* Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity
