rnastrand reading direction of structured rnas in multiple sequence alignmentsrnastrand阅读结构化的rna序列在多个方向对齐.pdfVIP

Algorithms for Molecular Biology BioMed Central Research Open Access RNAstrand: reading direction of structured RNAs in multiple sequence alignments 1 1,2,3 Kristin Reiche* and Peter F Stadler Address: 1Bioinformatics Group, Dept. of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria and 3Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA Email: Kristin Reiche* - kristin@bioinf.uni-leipzig.de; Peter F Stadler - studla@bioinf.uni-leipzig.de * Corresponding author Published: 31 May 2007 Received: 12 April 2007 Accepted: 31 May 2007 Algorithms for Molecular Biology 2007, 2:6 doi:10.1186/1748-7188-2-6 This article is available from: /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 (/licenses/by/2.0), 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 di