RNA Secondary Structure Prediction

The field of RNA secondary structure prediction matured in the last 10 years with the development of many readily available software packages. The thermodynamic parameters for predicting the free energy of an RNA secondary structure are continuing to be revised on the basis of new experiments. This article reviews the available secondary structure prediction algorithms for both a single sequence and multiple sequences. Keywords: RNA thermodynamics; RNA secondary structure; RNA statistical mechanics; folding free energy

[1]  D. Turner,et al.  Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. , 2000, Biochemistry.

[2]  Christian N. S. Pedersen,et al.  Fast evaluation of internal loops in RNA secondary structure prediction , 1999, Bioinform..

[3]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[4]  D. Turner,et al.  Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. , 2002, Biochemistry.

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

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

[7]  C. Lawrence,et al.  Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. , 2001, Nucleic acids research.

[8]  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.

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

[10]  E Westhof,et al.  Analysis of the cooperative thermal unfolding of the td intron of bacteriophage T4. , 1999, Nucleic acids research.

[11]  Joshua A Bittker,et al.  Recent advances in the in vitro evolution of nucleic acids. , 2002, Current opinion in chemical biology.

[12]  Christian N. S. Pedersen,et al.  RNA Pseudoknot Prediction in Energy-Based Models , 2000, J. Comput. Biol..

[13]  E Westhof,et al.  Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices. , 1997, Nucleic acids research.

[14]  R. Nussinov,et al.  Fast algorithm for predicting the secondary structure of single-stranded RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .

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

[17]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[18]  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.

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

[20]  Xin Wang,et al.  A novel sRNA component of the carbon storage regulatory system of Escherichia coli , 2003, Molecular microbiology.

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

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

[23]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

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

[25]  N. Pace,et al.  Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. , 2000, RNA.

[26]  J. M. Diamond,et al.  Thermodynamics of three-way multibranch loops in RNA. , 2001, Biochemistry.

[27]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

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

[29]  D. Turner,et al.  The energetics of small internal loops in RNA , 1999, Biopolymers.

[30]  M J Serra,et al.  A test of the model to predict unusually stable RNA hairpin loop stability. , 2000, RNA.

[31]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

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

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

[34]  Bryan R. Cullen,et al.  RNA interference: antiviral defense and genetic tool , 2002, Nature Immunology.

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

[36]  R. Jaenisch,et al.  RNA and the Epigenetic Regulation of X Chromosome Inactivation , 1998, Cell.

[37]  Niles A. Pierce,et al.  A partition function algorithm for nucleic acid secondary structure including pseudoknots , 2003, J. Comput. Chem..

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

[39]  Bjarne Knudsen,et al.  RNA secondary structure prediction using stochastic context-free grammars and evolutionary history , 1999, Bioinform..

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

[41]  Brent M. Znosko,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. , 2002, Biochemistry.

[42]  E Rivas,et al.  A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.

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

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

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

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

[47]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[48]  K. Dill,et al.  RNA folding energy landscapes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[50]  C. Pleij,et al.  The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.

[51]  D. Turner,et al.  Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[52]  D H Turner,et al.  Thermodynamic stabilities of internal loops with GU closing pairs in RNA. , 2001, Biochemistry.