accelerated probabilistic inference of rna structure evolution加速概率推理的rna结构进化.pdfVIP

BMC Bioinformatics BioMed Central Methodology article Open Access Accelerated probabilistic inference of RNA structure evolution Ian Holmes* Address: Department of Bioengineering, University of California, Berkeley CA 94720-1762, USA Email: Ian Holmes* - ihh@ * Corresponding author Published: 24 March 2005 Received: 30 April 2004 Accepted: 24 March 2005 BMC Bioinformatics 2005, 6:73 doi:10.1186/1471-2105-6-73 This article is available from: /1471-2105/6/73 © 2005 Holmes; 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 Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoffs 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results: We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs