Secondary structure prediction for aligned RNA sequences.

[1]  Kelly P. Williams,et al.  The tmRNA Website: invasion by an intron , 2002, Nucleic Acids Res..

[2]  M. Crespi,et al.  Translational and Structural Requirements of the Early Nodulin Gene enod40, a Short-Open Reading Frame-Containing RNA, for Elicitation of a Cell-Specific Growth Response in the Alfalfa Root Cortex , 2001, Molecular and Cellular Biology.

[3]  B L Maidak,et al.  The RDP-II (Ribosomal Database Project) , 2001, Nucleic Acids Res..

[4]  Yves Van de Peer,et al.  The European Large Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[5]  R. Gutell,et al.  A story: unpaired adenosine bases in ribosomal RNAs. , 2000, Journal of molecular biology.

[6]  Maciej Szymanski,et al.  Non-coding, mRNA-like RNAs database Y2K , 2000, Nucleic Acids Res..

[7]  Yves Van de Peer,et al.  The European Small Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

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

[9]  Christian Zwieb,et al.  SRPDB (Signal Recognition Particle Database) , 2000, Nucleic Acids Res..

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

[11]  V. Juan,et al.  RNA secondary structure prediction based on free energy and phylogenetic analysis. , 1999, Journal of molecular biology.

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

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

[14]  Peter F. Stadler,et al.  Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes , 1998, Comput. Chem..

[15]  R. Singer,et al.  RNA localization: different zipcodes, same postman? , 1998, Trends in cell biology.

[16]  M. Huynen,et al.  Automatic detection of conserved RNA structure elements in complete RNA virus genomes. , 1998, Nucleic acids research.

[17]  James W. Brown The ribonuclease P database , 1998, Nucleic Acids Res..

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

[19]  Gary D. Stormo,et al.  Automated Alignment of RNA Sequences to Pseudoknotted Structures , 1997, ISMB.

[20]  R. Lück,et al.  Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. , 1996, Journal of molecular biology.

[21]  Lawrence Hunter,et al.  Proceedings of the Pacific Symposium on Biocomputing '96. Hawaii, USA, 3-6 January 1996. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[22]  D. Haussler,et al.  Using multiple alignments and phylogenetic trees to detect RNA secondary structure. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[23]  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.

[24]  K. Han,et al.  Prediction of common folding structures of homologous RNAs. , 1993, Nucleic acids research.

[25]  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.

[26]  David K. Y. Chiu,et al.  Inferring consensus structure from nucleic acid sequences , 1991, Comput. Appl. Biosci..

[27]  M. Zuker,et al.  Predicting common foldings of homologous RNAs. , 1991, Journal of biomolecular structure & dynamics.

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

[29]  C R Woese,et al.  Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[32]  Paulien Hogeweg,et al.  Energy directed folding of RNA sequences , 1984, Nucleic Acids Res..

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

[34]  Jerrold R. Griggs,et al.  Algorithms for Loop Matchings , 1978 .