TAILIEUCHUNG - Báo cáo y học: "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"

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: Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. | Open Access Phylogenetic simulation of promoter evolution estimation and modeling of binding site turnover events and assessment of their impact on alignment tools Weichun Huang Joseph R Nevins and Uwe Ohler Addresses institute for Genome Sciences and Policy Duke University Durham NC 27708 USA. Current address Department of Biology Boston College Chestnut Hill MA 02467 USA. Correspondence Weichun Huang. Email . Uwe Ohler. Email Published 24 October 2007 Genome Biology 2007 8 R225 doi gb-2007-8- l0-r225 The electronic version of this article is the complete one and can be found online at http 2007 8 10 R225 Received 11 April 2007 Revised 20 October 2007 Accepted 24 October 2007 2007 Huang 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 Background The phenomenon of functional site turnover has important implications for the study of regulatory region evolution such as for promoter sequence alignments and transcription factor binding site TFBS identification. At present it remains difficult to estimate TFBS turnover rates on real genomic sequences as reliable mappings of functional sites across related species are often not available. As an alternative we introduce a flexible new simulation system Phylogenetic Simulation of Promoter Evolution PSPE designed to study functional site turnovers in regulatory sequences. Results Using PSPE we study replacement turnover rates of different individual TFBSs and simple modules of two sites under neutral evolutionary functional constraints. We find that TFBS replacement turnover can happen rapidly in promoters and turnover rates vary significantly among different TFBSs and modules. We assess the influence of

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