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algorithms for locating extremely conserved elements in multiple sequence alignments多序列比对算法定位极其保守元素.pdf

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algorithms for locating extremely conserved elements in multiple sequence alignments多序列比对算法定位极其保守元素

BMC Bioinformatics BioMed Central Research article Open Access Algorithms for locating extremely conserved elements in multiple sequence alignments Huei-Hun E Tseng1 and Martin Tompa*1,2 Addresses: 1Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA, 98195-2350, USA and 2Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA E-mail: Huei-Hun E Tseng - lachesis@; Martin Tompa* - tompa@ *Corresponding author Published: 18 December 2009 Received: 29 July 2009 Accepted: 18 December 2009 BMC Bioinformatics 2009, 10:432 doi: 10.1186/1471-2105-10-432 This article is available from: /1471-2105/10/432 © 2009 Tseng and Tompa; 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 Background: In 2004, Bejerano et al. announced the startling discovery of hundreds of “ultraconserved elements”, long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research. Results: We generalize the notion of ultraconserved element in a natural way from extraordinary human-rodent conservation to extraordinary conservation over an arbitrary set of species. We call these “Extremely Conserved Elements”. There is a linear time alg