Fast algorithms for computing sequence distances by exhaustive substring composition.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access Fast algorithms for computing sequence distances by exhaustive substring composition Alberto Apostolico*1,2,3 and Olgert Denas*3 Address: 1Academia Nazionale dei Lincei, Rome, Italy, 2Department of Information Engineering, Universitá di Padova, Padova, Italy and 3College of Computing, Georgia Institute of Technology, Atlanta, Georgia, USA Email: Alberto Apostolico* - axa@; Olgert Denas* - gerti@ * Corresponding authors Published: 28 October 2008 Received: 23 June 2008 Accepted: 28 October 2008 Algorithms for Molecular Biology 2008, 3:13 doi:10.1186/1748-7188-3-13 This article is available from: /content/3/1/13 ? 2008 Apostolico and Denas; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are hardly fulfilled by the more traditional measures of sequence similarity and distance, like string edit and gene rearrangement, due to a mixture of epistemological and computational problems. Alternative measures, based on the subword composition of sequences, have emerged in recent years and proved to be both fast and effective in a variety of tested cases. The common denominator of such measures is an underlying information theoretic notion of relative compressibility. Their viability depends critically on computational cost. The present paper describes as a paradigm the extension and efficient implementation of one of the methods in this class. The method is based on the comparison of the frequencies of all