Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Analysis of computational approaches for motif discovery. | Algorithms for Molecular Biology BioMed Central Research Analysis of computational approaches for motif discovery Nan Li and Martin Tompa Open Access Address Department of Computer Science and Engineering Box 352350 University of Washington Seattle WA 98195-2350 USA Email Nan Li - annli@ Martin Tompa - tompa@ Corresponding author Published 19 May 2006 Received 10 March 2006 Algorithms for Molecular Biology 2006 1 8 doi 1748-7188-1-8 Accepted 19 May 2006 This article is available from http content 1 1 8 2006 Li and Tompa 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 Recently we performed an assessment of 1 3 popular computational tools for discovery of transcription factor binding sites M. Tompa N. Li et al. Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites Nature Biotechnology Jan. 2005 . This paper contains follow-up analysis of the assessment results and raises and discusses some important issues concerning the state of the art in motif discovery methods 1. We categorize the objective functions used by existing tools and design experiments to evaluate whether any of these objective functions is the right one to optimize. 2. We examine various features of the data sets that were used in the assessment such as sequence length and motif degeneracy and identify which features make data sets hard for current motif discovery tools. 3. We identify an important feature that has not yet been used by existing tools and propose a new objective function that incorporates this feature. For the past decade research on identifying regulatory elements notably the binding sites for transcription factors has been very intense. The problem
