Quantifying similarity between motifs 英文参考文献.docVIP

Open Access M d 2007GuptaetVoal.lumeetho8, Issue 2, Article R24 Quantifying similarity between motifs Shobhit Gupta*, John A Stamatoyannopoulos*, Timothy L Bailey? and William Stafford Noble*? Addresses: *Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA. ?Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia. ?Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Box 352350, Seattle, WA 98105, USA. Correspondence: William Stafford Noble. Email: noble@ Published: 26 February 2007 Received: 13 September 2006 Revised: 5 January 2007 Accepted: 26 February 2007 Genome Biology 2007, 8:R24 (doi:10.1186/gb-2007-8-2-r24) The electronic version of this article is the complete one and can be found online at /2007/8/2/R24 ? 2007 Gupta et al.; 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. Quantifyinga pmoTtoifmqtuoemrysimilaritya.ll/opws forbetweenthe statismotifstical measurement of similarity between pairs of motifs, thereby enabling searching a motif database with Abstract A common question within the context of de novo motif discovery is whether a newly discovered, putative motif resembles any previously discovered motif in an existing database. To answer this question, we define a statistical measure of motif-motif similarity, and we describe an algorithm, called Tomtom, for searching a database of motifs with a given query motif. Experimental simulations demonstrate the accuracy of Tomtoms E values and its effectiveness in finding similar motifs. Background motif discovery. For example, imagine that you are given a collection of promoter regions from gene