tailieunhanh - Báo cáo y học: " Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Critical Care giúp cho các bạn có thêm kiến thức về ngành y học đề tài: Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. | Open Access Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs Andra Ivan Marc S Halfonn and Saurabh Sinha Addresses Department of Computer Science and Institute for Genomic Biology University of Illinois at Urbana-Champaign N. Goodwin Ave Urbana IL 61801 USA. Department of Biochemistry State University of New York at Buffalo Main St Buffalo NY 14214 USA. New York State Center of Excellence in Bioinformatics and the Life Sciences Ellicott St Buffalo NY 14203 USA. Correspondence Saurabh Sinha. Email sinhas@ Published 28 January 2008 Genome Biology 2008 9 R22 doi gb-2008-9-1 -r22 The electronic version of this article is the complete one and can be found online at http 2008 9 1 R22 Received 12 September 2007 Revised 18 December 2007 Accepted 28 January 2008 2008 Ivan 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 We consider the problem of predicting c s-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting and create over 30 new data sets using Drosoph la modules to use as a benchmark . We propose two new methods for the problem and evaluate these as well as two existing methods on our benchmark. We find that the challenge of predicting c s-regulatory modules ab initio without any input of relevant motifs is a realizable goal. Background Understanding the richness and complexity of the transcriptional network underlying the early stages of fruitfly development is a success story of developmental molecular biology. It is also an inspiration for bioinformaticians working on sequence analysis. This transcriptional regulatory network is implemented through cís-regulatory modules CRMs .