Predicting a set of minimal free energy RNA secondary structures common to two sequences

MOTIVATION Function derives from structure, therefore, there is need for methods to predict functional RNA structures. RESULTS The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low-energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20% of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence. AVAILABILITY Dynalign can be downloaded at http://rna.urmc.rochester.edu

[1]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[2]  M. Zuker,et al.  Using reliability information to annotate RNA secondary structures. , 1998, RNA.

[3]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[4]  P. Argos,et al.  Determination of reliable regions in protein sequence alignments. , 1990, Protein engineering.

[5]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[6]  D. Mathews Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.

[7]  Miroslawa Z. Barciszewska,et al.  5S ribosomal RNA database Y2K , 2000, Nucleic Acids Res..

[8]  Laurie J. Heyer,et al.  Finding the most significant common sequence and structure motifs in a set of RNA sequences. , 1997, Nucleic acids research.

[9]  M S Waterman,et al.  Sequence alignments in the neighborhood of the optimum with general application to dynamic programming. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[10]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[11]  Robert Giegerich,et al.  A comprehensive comparison of comparative RNA structure prediction approaches , 2004, BMC Bioinformatics.

[12]  Peter Walter,et al.  Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum , 1982, Nature.

[13]  Carl R. Woese,et al.  4 Probing RNA Structure, Function, and History by Comparative Analysis , 1993 .

[14]  A. Hüttenhofer,et al.  The expanding snoRNA world. , 2002, Biochimie.

[15]  R. Gutell,et al.  The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.

[16]  R. Knight,et al.  BayesFold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences , 2004 .

[17]  M Vingron,et al.  Near-optimal sequence alignment. , 1996, Current opinion in structural biology.

[18]  E Westhof,et al.  An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. , 1995, Journal of molecular biology.

[19]  D. Bartel,et al.  One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.

[20]  Detlev Riesner,et al.  Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation , 1997, The EMBO journal.

[21]  M. Zuker Suboptimal sequence alignment in molecular biology. Alignment with error analysis. , 1991, Journal of molecular biology.

[22]  D. Turner,et al.  Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. , 2002, Journal of molecular biology.

[23]  Jennifer A. Doudna,et al.  The chemical repertoire of natural ribozymes , 2002, Nature.

[24]  Thomas A Steitz,et al.  Structural insights into peptide bond formation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Rob Knight,et al.  BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. , 2004, RNA.

[26]  T. Cech,et al.  Analysis of the structure of Tetrahymena nuclear RNAs in vivo: telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. , 1995, RNA.

[27]  M. Zuker On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[28]  G. Knapp Enzymatic approaches to probing of RNA secondary and tertiary structure. , 1989, Methods in enzymology.

[29]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[30]  C. Lawrence,et al.  A statistical sampling algorithm for RNA secondary structure prediction. , 2003, Nucleic acids research.

[31]  R. Lück,et al.  ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. , 1999, Nucleic acids research.

[32]  S. Le,et al.  Prediction of common secondary structures of RNAs: a genetic algorithm approach. , 2000, Nucleic acids research.

[33]  J. Ebel,et al.  Probing the structure of RNAs in solution. , 1987, Nucleic acids research.

[34]  Christian Zwieb,et al.  The signal recognition particle database (SRPDB) , 1993, Nucleic Acids Res..

[35]  Sean R. Eddy,et al.  Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction , 2004, BMC Bioinformatics.

[36]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[37]  Weixiong Zhang,et al.  An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots , 2004, Bioinform..

[38]  Robert Giegerich,et al.  Abstract shapes of RNA. , 2004, Nucleic acids research.

[39]  Christian Zwieb,et al.  The Signal Recognition Particle Database (SRPDB) , 1993, Nucleic Acids Res..

[40]  M. Zuker,et al.  "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. , 1995, Nucleic acids research.

[41]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[42]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Peter F. Stadler,et al.  Alignment of RNA base pairing probability matrices , 2004, Bioinform..

[44]  I. Tinoco,et al.  How RNA folds. , 1999, Journal of molecular biology.

[45]  Hélène Touzet,et al.  Finding the common structure shared by two homologous RNAs , 2003, Bioinform..

[46]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[47]  D. Sankoff Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .