a specialized learner for inferring structured cis-regulatory modules专业学习者为推断结构基因模块.pdfVIP

BMC Bioinformatics BioMed Central Methodology article Open Access A specialized learner for inferring structured cis-regulatory modules Keith Noto*1,2 and Mark Craven 1,2 Address: 1Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA and 2Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA Email: Keith Noto* - noto@; Mark Craven - craven@ * Corresponding author Published: 05 December 2006 Received: 18 July 2006 Accepted: 05 December 2006 BMC Bioinformatics 2006, 7:528 doi:10.1186/1471-2105-7-528 This article is available from: /1471-2105/7/528 © 2006 Noto and Craven; 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: The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis- regulatory modules (CRMs). We present an expressive and easily comprehensible CRM representation which is capable of capturing several aspects of a CRMs structure and distinguishing between DNA sequences which do or do not contain it. We also present a learning algorithm tailored for this domain, and a novel method to avoid overfittin