The Vienna RNA Secondary Structure Server：（维也纳RNA二级结构的服务器）.pdfVIP

The Vienna RNA Secondary Structure Server Ivo L. Hofacker Institut f¨ur Theoretische Chemie und Molekulare Strukturbiologie, Universit¨at Wien, W¨ahringerstraße 17, A-1090 Wien, Austria Abstract The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences, and the design of sequences that will fold into a predefined structure. All three services can be accessed via the the Vienna RNA web server at http://rna.tbi.univie.ac.at/ Keywords: RNA secondary structure prediction, partition function, consensus struc- ture, sequence design. 1. Introduction Biomolecules exhibit a close interplay between structure and function. Therefore the growing number of RNA molecules with complex functions, beyond that of encod- ing proteins, has brought increased demand for RNA structure prediction methods. While prediction of tertiary structure is usually infeasible, the area of RNA secondary structures is an example where computational methods have been highly successful. The first practical dynamic programming algorithms to predict the optimal secondary structure of an RNA sequence date back over 20 years [16]. Since then they’ve been extended to allow prediction of suboptimal structures [14, 13] and thermodynamic ensembles [10], which allow to assign a confidence level or “well definedness” to the predictions [15]. Recently, several methods have addressed the problem of predicting a consensus struc- ture for a group of related RNA sequences [2, 3, 8, 6, 7, 4]. Such conserved structures are of p