Gräf S, Strothmann D, Kurtz S, Steger G: A computational approach to search for non-coding RNAs in large genomic data. In Small RNAs: Analysis and Regulatory functions of Nucleic Acids and Molecular Biology Series. Volume 17. Edited by: Nellen W, Hammann C. Springer Verlag; 2006:57–74.
Google Scholar
Klein R, Eddy S: RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinf 2003, 4: 44. 10.1186/1471-2105-4-44
Article
Google Scholar
Schöniger M, von Haeseler A: Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models. J Mol Evol 1999, 49: 691–698. 10.1007/PL00006590
Article
PubMed
Google Scholar
Wolf M, Achtziger M, Schultz J, Dandekar T, Müller T: Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA 2005, 11: 1616–1623. 10.1261/rna.2144205
Article
PubMed Central
CAS
PubMed
Google Scholar
Caetano-Anolles G: Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure. J Mol Evol 2005, 60: 635–652. 10.1007/s00239-004-0244-z
Article
CAS
PubMed
Google Scholar
Thompson J, Higgins D, Gibson T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22: 4673–4680. 10.1093/nar/22.22.4673
Article
PubMed Central
CAS
PubMed
Google Scholar
Gardner PP, Wilm A, Washietl S: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 2005, 33: 2433–2439. 10.1093/nar/gki541
Article
PubMed Central
CAS
PubMed
Google Scholar
Mathews D, Turner D: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 2002, 317: 191–203. 10.1006/jmbi.2001.5351
Article
CAS
PubMed
Google Scholar
Havgaard J, Lyngso R, Gorodkin J: The foldalign web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res 2005, 33: W650–653. 10.1093/nar/gki473
Article
PubMed Central
CAS
PubMed
Google Scholar
Hofacker I, Bernhart S, Stadler P: Alignment of RNA base pairing probability matrices. Bioinformatics 2004, 20: 2222–2227. 10.1093/bioinformatics/bth229
Article
CAS
PubMed
Google Scholar
Holmes I: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 2005, 6: 73. 10.1186/1471-2105-6-73
Article
PubMed Central
PubMed
Google Scholar
Sankoff D: Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J Appl Math 1985, 45: 810–825. 10.1137/0145048
Article
Google Scholar
Seibel P, Müller T, Dandekar T, Schultz J, Wolf M: 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 2006, 7: 498. 10.1186/1471-2105-7-498
Article
PubMed Central
PubMed
Google Scholar
Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J: Semiautomated improvement of RNA alignments. RNA 2007, 13(11):1850–1859. 10.1261/rna.215407
Article
PubMed Central
CAS
PubMed
Google Scholar
Jossinet F, Westhof E: Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 2005, 21: 3320–3321. 10.1093/bioinformatics/bti504
Article
CAS
PubMed
Google Scholar
Lück R, Gräf S, Steger G: CONSTRUCT: a tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res 1999, 27: 4208–4217. 10.1093/nar/27.21.4208
Article
PubMed Central
PubMed
Google Scholar
Hofacker IL, Fekete M, Stadler PF: Secondary structure prediction for aligned RNA sequences. J Mol Biol 2002, 319: 1059–1066. 10.1016/S0022-2836(02)00308-X
Article
CAS
PubMed
Google Scholar
Ruan J, Stormo GD, Zhang W: An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 2004, 20: 58–66. 10.1093/bioinformatics/btg373
Article
CAS
PubMed
Google Scholar
Griffths-Jones S: RALEE-RNA ALignment editor in Emacs. Bioinformatics 2005, 21: 257–259. 10.1093/bioinformatics/bth489
Article
Google Scholar
Katoh K, Kuma Ki, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33: 511–518. 10.1093/nar/gki198
Article
PubMed Central
CAS
PubMed
Google Scholar
Dalli D, Wilm A, Mainz I, Steger G: StrAl: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics 2006, 22: 1593–1599. 10.1093/bioinformatics/btl142
Article
CAS
PubMed
Google Scholar
Bellamy-Royds A, Turcotte M: Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction? BMC Bioinformatics 2007, 8: 190. 10.1186/1471-2105-8-190
Article
PubMed Central
PubMed
Google Scholar
Hofacker I: Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31: 3429–3431. 10.1093/nar/gkg599
Article
PubMed Central
CAS
PubMed
Google Scholar
Tinoco I Jr, Uhlenbeck O, Levine M: Estimation of secondary structure in ribonucleic acids. Nature 1971, 230: 362–367. 10.1038/230362a0
Article
CAS
PubMed
Google Scholar
Witwer C, Hofacker I, Stadler P: Prediction of consensus RNA secondary structures including pseu-doknots. IEEE/ACM Trans Comput Biol Bioinform 2004, 1: 66–77. 10.1109/TCBB.2004.22
Article
CAS
PubMed
Google Scholar
Chiu D, Kolodziejczak T: Inferring consensus structure from nucleic acid sequences. Comp Appl Biosci 1991, 7: 347–352.
CAS
PubMed
Google Scholar
Martin LC, Gloor GB, Dunn SD, Wahl LM: Using information theory to search for co-evolving residues in proteins. Bioinformatics 2005, 21: 4116–4124. 10.1093/bioinformatics/bti671
Article
CAS
PubMed
Google Scholar
Gutell R, Power A, Hertz G, Putz E, Stormo G: Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 1992, 20: 5785–5795. 10.1093/nar/20.21.5785
Article
PubMed Central
CAS
PubMed
Google Scholar
Schneider T, Stormo G, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. J Mol Biol 1986, 188: 415–431. 10.1016/0022-2836(86)90165-8
Article
CAS
PubMed
Google Scholar
Lindgreen S, Gardner P, Krogh A: Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics 2006, 22: 2988–2995. 10.1093/bioinformatics/btl514
Article
CAS
PubMed
Google Scholar
Lescoute A, Leontis N, Massire C, Westhof E: Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Res 2005, 33: 2395–2409. 10.1093/nar/gki535
Article
PubMed Central
CAS
PubMed
Google Scholar
Nussinov R, Pieczenik G, Griggs J, Kleitman D: Algorithms for loop matchings. SIAM J Appl Math 1978, 35: 68–82. 10.1137/0135006
Article
Google Scholar
Steger G, Hofmann H, Förtsch J, Gross H, Randles J, Sänger H, Riesner D: Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data. J Biomol Struct Dyn 1984, 2: 543–571.
Article
CAS
PubMed
Google Scholar
Zuker M: On finding all suboptimal foldings of an RNA molecule. Science 1989, 244: 48–52. 10.1126/science.2468181
Article
CAS
PubMed
Google Scholar
Tabaska J, Cary R, Gabow H, Stormo G: An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics 1998, 14: 691–699. 10.1093/bioinformatics/14.8.691
Article
CAS
PubMed
Google Scholar
De Rijk P, De Wachter R: RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res 1997, 25: 4679–4684. 10.1093/nar/25.22.4679
Article
PubMed Central
CAS
PubMed
Google Scholar
Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31: 3406–3415. 10.1093/nar/gkg595
Article
PubMed Central
CAS
PubMed
Google Scholar
Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F: RNAML: a standard syntax for exchanging RNA information. RNA 2002, 8: 707–717. 10.1017/S1355838202028017
Article
PubMed Central
CAS
PubMed
Google Scholar
Gorodkin J, Heyer L, Brunak S, Stormo G: Displaying the information contents of structural RNA alignments: the structure logos. Comp Appl Biosci/Bioinformatics 1997, 13: 583–586.
CAS
Google Scholar
Gardner P, Giegerich R: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004, 5: 140. 10.1186/1471-2105-5-140
Article
PubMed Central
PubMed
Google Scholar
Eddy SR: SQUID – C function library for sequence analysis.2005. [http://selab.janelia.org/software.html]
Google Scholar
Bernhart SH, Hofacker IL, Stadler PF: Local RNA base pairing probabilities in large sequences. Bioin-formatics 2006, 22: 614–615.
Article
CAS
Google Scholar
Kryukov GV, Gladyshev VN: The prokaryotic selenoproteome. EMBO Rep 2004, 5: 538–543. 10.1038/sj.embor.7400126
Article
PubMed Central
CAS
PubMed
Google Scholar
Hellen C, Sarnow P: Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev 2001, 15: 1593–1612. 10.1101/gad.891101
Article
CAS
PubMed
Google Scholar
Nishiyama T, Yamamoto H, Shibuya N, Hatakeyama Y, Hachimori A, Uchiumi T, Nakashima N: Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res 2003, 31: 2434–2442. 10.1093/nar/gkg336
Article
PubMed Central
CAS
PubMed
Google Scholar
Spahn C, Jan E, Mulder A, Grassucci R, Sarnow P, Frank J: Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell 2004, 118: 465–475. 10.1016/j.cell.2004.08.001
Article
CAS
PubMed
Google Scholar
Schüler M, Connell S, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek P, Westhof E, Spahn C: Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol 2006, 13: 1092–1096. 10.1038/nsmb1177
Article
PubMed
Google Scholar
Pfingsten J, Costantino D, Kieft J: Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science 2006, 314: 1450–1454. 10.1126/science.1133281
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanamori Y, Nakashima N: A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 2001, 7: 266–274. 10.1017/S1355838201001741
Article
PubMed Central
CAS
PubMed
Google Scholar
Griffths-Jones S, Bateman A, Marshall M, Khanna A, Eddy S: Rfam: an RNA family database. Nucleic Acids Res 2003, 31: 439–441. 10.1093/nar/gkg006
Article
Google Scholar
Griffths-Jones S, Moxon S, Marshall M, Khanna A, Eddy S, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, 33: D121-D124. 10.1093/nar/gki081
Article
Google Scholar
Meyer I, Miklós I: SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol 2007, 3: e149. 10.1371/journal.pcbi.0030149
Article
PubMed Central
PubMed
Google Scholar
Will S, Reiche K, Hofacker I, Stadler P, Backofen R: Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007, 3: e65. 10.1371/journal.pcbi.0030065
Article
PubMed Central
PubMed
Google Scholar
Torarinsson E, Havgaard JH, Gorodkin J: Multiple structural alignment and clustering of RNA sequences. Bioinformatics 2007, 23: 926–932. 10.1093/bioinformatics/btm049
Article
CAS
PubMed
Google Scholar
Kiryu H, Tabei Y, Kin T, Asai K: Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 2007, 23: 1588–1598. 10.1093/bioinformatics/btm146
Article
CAS
PubMed
Google Scholar
Zuker M: Calculating nucleic acid secondary structure. Curr Opin Struct Biol 2000, 10: 303–310. 10.1016/S0959-440X(00)00088-9
Article
CAS
PubMed
Google Scholar
Pace N, Thomas B, Woese C: Probing RNA structure, function, and history by comparative analysis. In The RNA World. Edited by: Gesteland R, Cech T, Atkins J. New York: Cold Spring Harbor Laboratory Press; 1999:113–141.
Google Scholar
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R: Beyond Mfold: Recent advances in RNA bioinformatics. J Biotech 2006, 124: 41–55. 10.1016/j.jbiotec.2006.01.034
Article
CAS
Google Scholar
Freyhult E, Bollback J, Gardner P: Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 2007, 17: 117–125. 10.1101/gr.5890907
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilm A, Mainz I, Steger G: An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol 2006, 1: 19. 10.1186/1748-7188-1-19
Article
PubMed Central
PubMed
Google Scholar
Dsouza M, Larsen N, Overbeek R: Searching for patterns in genomic data. Trends Genet 1997, 13: 497–498. 10.1016/S0168-9525(97)01347-4
Article
CAS
PubMed
Google Scholar
Nawrocki E, Eddy S: Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007, 3: e56. 10.1371/journal.pcbi.0030056
Article
PubMed Central
PubMed
Google Scholar
Ehresmann C, Baudin F, Mougel M, Romby P, Ebel J, Ehresmann B: Probing the structure of RNAs in solution. Nucleic Acids Res 1987, 15: 9109–9128. 10.1093/nar/15.22.9109
Article
PubMed Central
CAS
PubMed
Google Scholar
Tullius T, Greenbaum J: Mapping nucleic acid structure by hydroxyl radical cleavage. Curr Opin Chem Biol 2005, 9: 127–134. 10.1016/j.cbpa.2005.02.009
Article
CAS
PubMed
Google Scholar
Steger G: Secondary Structure Prediction. In Handbook of RNA Biochemistry. Edited by: Bindereif A, Hartmann R, Schön A, Westhof E. Wiley-VCH; 2004:513–535.
Google Scholar
Knight J: SEQIO: A C package for reading and writing sequences. 1996.
Google Scholar