A comprehensive comparison of comparative RNA structure prediction approaches
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[1] Robert Giegerich,et al. Prediction and Visualization of Structural Switches in RNA , 1998, Pacific Symposium on Biocomputing.
[2] I. Tinoco,et al. RNA folding and unfolding. , 2004, Current opinion in structural biology.
[3] R. Breaker,et al. Gene regulation by riboswitches , 2004, Nature Reviews Molecular Cell Biology.
[4] Jerrold R. Griggs,et al. Algorithms for Loop Matchings , 1978 .
[5] Pierre Baldi,et al. Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..
[6] Robert Giegerich,et al. Pure multiple RNA secondary structure alignments: a progressive profile approach , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[7] Tao Jiang,et al. A more efficient approximation scheme for tree alignment , 1997, RECOMB '97.
[8] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[9] M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.
[10] S. P. Fodor,et al. Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.
[11] Ceslovas Venclovas,et al. Assessment of progress over the CASP experiments , 2003, Proteins.
[12] Sean R. Eddy,et al. Rfam: an RNA family database , 2003, Nucleic Acids Res..
[13] David K. Y. Chiu,et al. Inferring consensus structure from nucleic acid sequences , 1991, Comput. Appl. Biosci..
[14] R. Gutell,et al. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. , 1995, RNA.
[15] D. Turner,et al. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. , 2002, Journal of molecular biology.
[16] Sean R. Eddy,et al. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure , 2002, BMC Bioinformatics.
[17] Roland L. Dunbrack,et al. CAFASP2: The second critical assessment of fully automated structure prediction methods , 2001, Proteins.
[18] Robert Giegerich,et al. Evaluating the predictability of conformational switching in RNA , 2004, Bioinform..
[19] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[20] Erik L L Sonnhammer,et al. Quality assessment of multiple alignment programs , 2002, FEBS letters.
[21] Kaizhong Zhang,et al. Comparing multiple RNA secondary structures using tree comparisons , 1990, Comput. Appl. Biosci..
[22] Olivier Poch,et al. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations , 2001, Nucleic Acids Res..
[23] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[24] Gary D. Stormo,et al. Identification of consensus patterns in unaligned DNA sequences known to be functionally related , 1990, Comput. Appl. Biosci..
[25] Elena Rivas,et al. The language of RNA: a formal grammar that includes pseudoknots , 2000, Bioinform..
[26] Robert Giegerich,et al. Local similarity in RNA secondary structures , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.
[27] D. Mathews. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.
[28] R. Guigó,et al. Evaluation of gene structure prediction programs. , 1996, Genomics.
[29] Carl R. Woese,et al. 4 Probing RNA Structure, Function, and History by Comparative Analysis , 1993 .
[30] C. Lawrence,et al. A statistical sampling algorithm for RNA secondary structure prediction. , 2003, Nucleic acids research.
[31] Jan Krüger,et al. RNA-related tools on the Bielefeld Bioinformatics Server , 2003, Nucleic Acids Res..
[32] Sean R. Eddy,et al. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction , 2004, BMC Bioinformatics.
[33] Xing Xu,et al. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences , 2004, Bioinform..
[34] Yves Van de Peer,et al. The European database on small subunit ribosomal RNA , 2002, Nucleic Acids Res..
[35] Jamie J. Cannone,et al. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction , 2004, BMC Bioinformatics.
[36] Peter F. Stadler,et al. Alignment of RNA base pairing probability matrices , 2004, Bioinform..
[37] O. Gotoh,et al. Multiple sequence alignment: algorithms and applications. , 1999, Advances in biophysics.
[38] 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.
[39] C Venclovas,et al. Some measures of comparative performance in the three CASPs , 1999, Proteins.
[40] Jennifer A. Doudna,et al. The chemical repertoire of natural ribozymes , 2002, Nature.
[41] Robert Giegerich,et al. Abstract shapes of RNA. , 2004, Nucleic acids research.
[42] Hélène Touzet,et al. CARNAC: folding families of related RNAs , 2004, Nucleic Acids Res..
[43] James W. Brown. The ribonuclease P database , 1998, Nucleic Acids Res..
[44] Sean R. Eddy,et al. RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.
[45] G. Stormo,et al. Discovering common stem-loop motifs in unaligned RNA sequences. , 2001, Nucleic acids research.
[46] G. Soukup,et al. Riboswitches exert genetic control through metabolite-induced conformational change. , 2004, Current opinion in structural biology.
[47] G. Stormo,et al. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. , 1992, Nucleic acids research.
[48] P. Higgs. RNA secondary structure: physical and computational aspects , 2000, Quarterly Reviews of Biophysics.
[49] Kaizhong Zhang,et al. Simple Fast Algorithms for the Editing Distance Between Trees and Related Problems , 1989, SIAM J. Comput..
[50] Thomas Dandekar,et al. Riboswitch finder tool for identification of riboswitch RNAs , 2004, Nucleic Acids Res..
[51] J. Mattick. Non‐coding RNAs: the architects of eukaryotic complexity , 2001, EMBO reports.
[52] D. Sankoff. Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .
[53] D. S. Fields,et al. An analysis of large rRNA sequences folded by a thermodynamic method. , 1996, Folding & design.
[54] S. Cawley,et al. Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.
[55] P. Stadler,et al. Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.
[56] David Penny,et al. Relics from the RNA World , 1998, Journal of Molecular Evolution.
[57] Roland L. Dunbrack,et al. CAFASP3: The third critical assessment of fully automated structure prediction methods , 2003, Proteins.
[58] Hélène Touzet,et al. Finding the common structure shared by two homologous RNAs , 2003, Bioinform..
[59] R. Guigó,et al. An assessment of gene prediction accuracy in large DNA sequences. , 2000, Genome research.
[60] Olivier Poch,et al. A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..
[61] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[62] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[63] Robert Giegerich,et al. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics , 2004, BMC Bioinformatics.
[64] Gary D. Stormo,et al. Displaying the information contents of structural RNA alignments: the structure logos , 1997, Comput. Appl. Biosci..
[65] Fatima Cvrčková,et al. Molecular diversity of phospholipase D in angiosperms , 2002, BMC Genomics.
[66] M. Hentze,et al. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[67] Kaizhong Zhang,et al. Alignment between Two RNA Structures , 2001, MFCS.
[68] Rolf Backofen,et al. MARNA: A server for multiple alignment of RNAs , 2003, German Conference on Bioinformatics.
[69] Olivier Poch,et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..
[70] Bin Ma,et al. A General Edit Distance between RNA Structures , 2002, J. Comput. Biol..
[71] J. Mattick,et al. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. , 2001, Molecular biology and evolution.
[72] Bruce A. Shapiro,et al. An algorithm for comparing multiple RNA secondary structures , 1988, Comput. Appl. Biosci..
[73] Laurie J. Heyer,et al. Finding the most significant common sequence and structure motifs in a set of RNA sequences. , 1997, Nucleic acids research.
[74] J. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.
[75] Mike A. Steel,et al. Metrics on RNA Secondary Structures , 2000, J. Comput. Biol..
[76] Bjarne Knudsen,et al. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history , 1999, Bioinform..
[77] S. Cawley,et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.
[78] Kuo-Chung Tai,et al. The Tree-to-Tree Correction Problem , 1979, JACM.
[79] Weixiong Zhang,et al. An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots , 2004, Bioinform..
[80] Walter Fontana,et al. Fast folding and comparison of RNA secondary structures , 1994 .
[81] RNA–Related Tools , 1994, Bio/Technology.
[82] Niles A. Pierce,et al. A partition function algorithm for nucleic acid secondary structure including pseudoknots , 2003, J. Comput. Chem..
[83] Christian N. S. Pedersen,et al. Fast evaluation of internal loops in RNA secondary structure prediction , 1999, Bioinform..
[84] P. Schuster,et al. Statistics of RNA secondary structures , 1993, Biopolymers.
[85] R. Gutell,et al. The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.
[86] István Miklós,et al. Co-transcriptional folding is encoded within RNA genes , 2004, BMC Molecular Biology.
[87] M. Gelfand,et al. Riboswitches: the oldest mechanism for the regulation of gene expression? , 2004, Trends in genetics : TIG.
[88] Tao Jiang,et al. Alignment of Trees - An Alternative to Tree Edit , 1994, Theor. Comput. Sci..
[89] I. Tinoco,et al. How RNA folds. , 1999, Journal of molecular biology.
[90] C Venclovas,et al. Comparison of performance in successive CASP experiments , 2001, Proteins.
[91] H. Schwalbe,et al. NMR Spectroscopy of RNA , 2003, Chembiochem : a European journal of chemical biology.
[92] Bjarne Knudsen,et al. Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .
[93] Yves Van de Peer,et al. The European Large Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..
[94] D. Penny,et al. The Path from the RNA World , 1998, Journal of Molecular Evolution.