tailieunhanh - Báo cáo sinh học: "RNAstrand: reading direction of structured RNAs in multiple sequence alignments."

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: RNAstrand: reading direction of structured RNAs in multiple sequence alignments. | Algorithms for Molecular Biology BioMed Central Research Open Access RNAstrand reading direction of structured RNAs in multiple sequence alignments Kristin Reiche 1 and Peter F Stadler1 2 3 Address 1Bioinformatics Group Dept. of Computer Science and Interdisciplinary Center for Bioinformatics University of Leipzig Hartelstrafie 16-18 D-04107 Leipzig Germany 2Institute for Theoretical Chemistry University of Vienna Wahringerstrafie 17 A-1090 Wien Austria and 3Santa Fe Institute 1399 Hyde Park Rd. Santa Fe NM 87501 USA Email Kristin Reiche - kristin@ Peter F Stadler - studla@ Corresponding author Published 31 May 2007 Received 12 April 2007 Algorithms for Molecular Biology 2007 2 6 doi 1748-7188-2-6 Accepted 3 I May 2007 This article is available from http content 2 1 6 2007 Reiche and Stadler 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 Motivation Genome-wide screens for structured ncRNA genes in mammals urochordates and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. Results While folding energies of an RNA and its reverse complement are similar the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. Software RNAstrand is freely available as a stand-alone tool from http .

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