Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: Quantifying similarity between motifs. | Method Open Access 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 Genome Biology 2007 8 R24 doi 186 gb-2007-8-2-r24 The electronic version of this article is the complete one and can be found online at http 2007 8 2 R24 Received 13 September 2006 Revised 5 January 2007 Accepted 26 February 2007 2007 Gupta et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 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 Tomtom s E values and its effectiveness in finding similar motifs. Background Discovering and characterizing DNA and protein sequence motifs are fundamental problems in computational biology. Here we use the term motif to refer to a position-specific probability matrix that describes a short sequence of amino acids or nucleotides that is important to the functioning of the cell. For example the regulation of transcription requires .
