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Volumn 36, Issue 20, 2008, Pages 6355-6362

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SINGLE STRANDED RNA;

EID: 56649099274     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn544     Document Type: Article
Times cited : (75)

References (57)
  • 2
    • 0028249154 scopus 로고
    • Prediction of RNA secondary structure by energy minimization
    • Zuker,M. (1994) Prediction of RNA secondary structure by energy minimization. Methods Mol. Biol., 25, 267-294.
    • (1994) Methods Mol. Biol , vol.25 , pp. 267-294
    • Zuker, M.1
  • 3
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • Do,C.B., Woods,D.A. and Batzoglou,S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98.
    • (2006) Bioinformatics , vol.22
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 4
    • 29844435528 scopus 로고    scopus 로고
    • A computational screen for mammalian pseudouridylation guide H/ACA RNAs
    • Schattner,P., Barberan-Soler,S. and Lowe,T.M. (2006) A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA, 12, 15-25.
    • (2006) RNA , vol.12 , pp. 15-25
    • Schattner, P.1    Barberan-Soler, S.2    Lowe, T.M.3
  • 5
    • 38449092636 scopus 로고    scopus 로고
    • SnoReport: Computational identi.cation of snoRNAs with unknown targets
    • Hertel,J., Hofacker,I.L. and Stadler,P.F. (2007) SnoReport: computational identi.cation of snoRNAs with unknown targets. Bioinformatics, 24, 158-164.
    • (2007) Bioinformatics , vol.24 , pp. 158-164
    • Hertel, J.1    Hofacker, I.L.2    Stadler, P.F.3
  • 6
    • 36448982884 scopus 로고    scopus 로고
    • PSSMTS: Position specific scoring matrices on tree structures
    • Sato,K., Morita,K. and Sakakibara,Y. (2008) PSSMTS: Position specific scoring matrices on tree structures. J. Math. Biol., 56, 201-214.
    • (2008) J. Math. Biol , vol.56 , pp. 201-214
    • Sato, K.1    Morita, K.2    Sakakibara, Y.3
  • 7
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
    • (1985) SIAM J. Appl. Math , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 8
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • Gardner,P.P. and Giegerich,R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140.
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 9
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most significant common sequence and structure motifs in a set of RNA sequences
    • Gorodkin,J., Heyer,L. and Stormo,G. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res., 25, 3724-3732.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3724-3732
    • Gorodkin, J.1    Heyer, L.2    Stormo, G.3
  • 10
    • 23144449520 scopus 로고    scopus 로고
    • The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
    • Web Server Issue, W650-W653
    • Havgaard,J.H., Lyngso,R.B. and Gorodkin,J. (2005) The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res., 33 (Web Server Issue), W650-W653.
    • (2005) Nucleic Acids Res , vol.33
    • Havgaard, J.H.1    Lyngso, R.B.2    Gorodkin, J.3
  • 11
    • 34249699636 scopus 로고    scopus 로고
    • Multiple structural alignment and clustering of RNA sequences
    • Torarinsson,E., Havgaard,J.H. and Gorodkin,J. (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics, 23 926-932.
    • (2007) Bioinformatics , vol.23 , pp. 926-932
    • Torarinsson, E.1    Havgaard, J.H.2    Gorodkin, J.3
  • 12
    • 35748971022 scopus 로고    scopus 로고
    • Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
    • Havgaard,J.H., Torarinsson,E. and Gorodkin,J. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908.
    • (2007) PLoS Comput. Biol , vol.3 , pp. 1896-1908
    • Havgaard, J.H.1    Torarinsson, E.2    Gorodkin, J.3
  • 13
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews,D.H. and Turner,D.H. (2002) Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 317, 191-203.
    • (2002) J. Mol. Biol , vol.317 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 14
    • 34248632816 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
    • Harmanci,A.O., Sharma,G. and Mathews,D.H. (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics, 8, 130.
    • (2007) BMC Bioinformatics , vol.8 , pp. 130
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 15
    • 5044242515 scopus 로고    scopus 로고
    • Alignment of RNA base pairing probability matrices
    • Hofacker,I.L., Bernhart,S.H. and Stadler,P.F. (2004) Alignment of RNA base pairing probability matrices. Bioinformatics, 20, 2222-2227.
    • (2004) Bioinformatics , vol.20 , pp. 2222-2227
    • Hofacker, I.L.1    Bernhart, S.H.2    Stadler, P.F.3
  • 17
    • 34247598415 scopus 로고    scopus 로고
    • Inferring Non-Coding RNA families and classes by means of genome-scale structure-based clustering
    • Will,S., Reiche,K., Hofacker,I.L., Stadler,P.F. and Backofen,R. (2007) Inferring Non-Coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Comput. Biol. 3, e65.
    • (2007) PLOS Comput. Biol , vol.3
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 18
    • 42449109109 scopus 로고    scopus 로고
    • PARTS: Probabilistic alignment for RNA joinT secondary structure prediction
    • Harmanci,A.O., Sharma,G. and Mathews,D.H. (2008) PARTS: Probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Res., 36, 2406-2417.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2406-2417
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 19
    • 25444433586 scopus 로고    scopus 로고
    • Accelerated probabilistic inference of RNA structure evolution
    • Holmes,I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 6, 73.
    • (2005) BMC Bioinformatics , vol.6 , pp. 73
    • Holmes, I.1
  • 20
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • Dowell,R.D. and Eddy,S.R. (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics, 7, 400.
    • (2006) BMC Bioinformatics , vol.7 , pp. 400
    • Dowell, R.D.1    Eddy, S.R.2
  • 21
    • 32544452741 scopus 로고    scopus 로고
    • CMfinder - a covariance model based RNA motif finding algorithm
    • Yao,Z., Weinberg,Z. and Ruzzo,W.L. (2006) CMfinder - a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452.
    • (2006) Bioinformatics , vol.22 , pp. 445-452
    • Yao, Z.1    Weinberg, Z.2    Ruzzo, W.L.3
  • 22
    • 34548443728 scopus 로고    scopus 로고
    • SimulFold: Simultaneously inferring RNA structures including pseudoknots, alignments and trees using a Bayesian MCMC framework
    • Meyer,I.M. and Miklos,I. (2007) SimulFold: Simultaneously inferring RNA structures including pseudoknots, alignments and trees using a Bayesian MCMC framework. PLoS Comput. Biol., 3, e149.
    • (2007) PLoS Comput. Biol , vol.3
    • Meyer, I.M.1    Miklos, I.2
  • 25
    • 33745590704 scopus 로고    scopus 로고
    • Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure
    • Torarinsson,E., Sawera,M., Havgaard,J.H., Fredholm,M. and Gorodkin,J. (2006) Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res., 16, 885-889.
    • (2006) Genome Res , vol.16 , pp. 885-889
    • Torarinsson, E.1    Sawera, M.2    Havgaard, J.H.3    Fredholm, M.4    Gorodkin, J.5
  • 26
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • Gardner,P.P., Wilm,A. and Washietl,S. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33, 2433-2439.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2433-2439
    • Gardner, P.P.1    Wilm, A.2    Washietl, S.3
  • 27
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knuds,en,B. and Hein,J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knuds1    en, B.2    Hein, J.3
  • 28
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 29
    • 42149083815 scopus 로고    scopus 로고
    • Centroid estimation in discrete high-dimensional spaces with applications in biology
    • Carvalho,L.E. and Lawrence,C.E. (2008) Centroid estimation in discrete high-dimensional spaces with applications in biology. Proc. Natl. Acad. Sci. USA, 105, 3209-3214.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 3209-3214
    • Carvalho, L.E.1    Lawrence, C.E.2
  • 30
    • 0029595355 scopus 로고
    • A reliable sequence alignment method based on probabilities of residue correspondences
    • Miyazawa,S. (1995) A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng., 8, 999-1009.
    • (1995) Protein Eng , vol.8 , pp. 999-1009
    • Miyazawa, S.1
  • 31
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do,C.B., Mahabhashyam,M.S.P., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 32
    • 35048841224 scopus 로고    scopus 로고
    • The Partition Function Variant of Sankoff's Algorithm
    • Springer, Heidelberg
    • Hofacker,I.L. and Stadler,P.F. (2004) The Partition Function Variant of Sankoff's Algorithm. Lecture Notes in Computer Science LNCS 3039. Springer, Heidelberg.
    • (2004) Lecture Notes in Computer Science LNCS , vol.3039
    • Hofacker, I.L.1    Stadler, P.F.2
  • 33
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • Knudsen,B. and Hein,J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15(6), 446-454.
    • (1999) Bioinformatics , vol.15 , Issue.6 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 34
    • 33847262911 scopus 로고    scopus 로고
    • Robust prediction of consensus secondary structures using averaged base pairing probability matrices
    • Kiryu,H., Kin,T. and Asai,K. (2007) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics, 23, 434-441.
    • (2007) Bioinformatics , vol.23 , pp. 434-441
    • Kiryu, H.1    Kin, T.2    Asai, K.3
  • 35
    • 33744945759 scopus 로고    scopus 로고
    • Identification of consensus RNA secondary structures using suffix arrays
    • Anwar,M., Nguyen,T. and Turcotte,M. (2006) Identification of consensus RNA secondary structures using suffix arrays. BMC Bioinformatics, 7, 244.
    • (2006) BMC Bioinformatics , vol.7 , pp. 244
    • Anwar, M.1    Nguyen, T.2    Turcotte, M.3
  • 36
    • 33645984848 scopus 로고    scopus 로고
    • Consensus folding of unaligned RNA sequences revisited
    • Bafna,V., Tang,H. and Zhang,S. (2006) Consensus folding of unaligned RNA sequences revisited. J. Comput. Biol. 13, 283-295.
    • (2006) J. Comput. Biol , vol.13 , pp. 283-295
    • Bafna, V.1    Tang, H.2    Zhang, S.3
  • 37
    • 33749845559 scopus 로고    scopus 로고
    • Mining frequent stem patterns from unaligned RNA sequences
    • Hamada,M., Tsuda,K., Kudo,T., Kin, T. and Asai, K. (2006) Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics 22, 2480-2487.
    • (2006) Bioinformatics , vol.22 , pp. 2480-2487
    • Hamada, M.1    Tsuda, K.2    Kudo, T.3    Kin, T.4    Asai, K.5
  • 38
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker,I.L., Fekete,M. and Stadler,P.F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
    • (2002) J. Mol. Biol , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 39
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    • Dowell,R.D. and Eddy,S.R. (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics, 5, 71.
    • (2004) BMC Bioinformatics , vol.5 , pp. 71
    • Dowell, R.D.1    Eddy, S.R.2
  • 42
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 43
    • 0035873307 scopus 로고    scopus 로고
    • Discovering Common Stem-Loop Motifs in Unaligned RNA Sequences
    • Gorodkin,J., Stricklin,S.L. and Stormo,G.D. (2001) Discovering Common Stem-Loop Motifs in Unaligned RNA Sequences. Nucleic Acids Res., 29, 2135-2144.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2135-2144
    • Gorodkin, J.1    Stricklin, S.L.2    Stormo, G.D.3
  • 44
    • 9544250384 scopus 로고    scopus 로고
    • Comparing two K-category assignments by a K-category correlation coefficient
    • Gorodkin,J. (2004) Comparing two K-category assignments by a K-category correlation coefficient. Comput. Biol. Chem., 28, 367-374.
    • (2004) Comput. Biol. Chem , vol.28 , pp. 367-374
    • Gorodkin, J.1
  • 45
    • 0028953185 scopus 로고
    • The sequence of the stem and flanking sequences at the 30 end of histone mRNA are critical determinants for the binding of the stem-loop binding protein
    • Williams,A.S. and Marzlu.,W.F. (1995) The sequence of the stem and flanking sequences at the 30 end of histone mRNA are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Res., 23, 654-662.
    • (1995) Nucleic Acids Res , vol.23 , pp. 654-662
    • Williams, A.S.1    Marzlu, W.F.2
  • 46
    • 0031762554 scopus 로고    scopus 로고
    • The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication
    • McKnight,K.L. and Lemon,S.M. (1998) The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication. RNA, 4, 1569-1584.
    • (1998) RNA , vol.4 , pp. 1569-1584
    • McKnight, K.L.1    Lemon, S.M.2
  • 48
    • 6844266251 scopus 로고    scopus 로고
    • A common RNA motif in the 30 end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus
    • Jonassen,C.M., Jonassen,T.O. and Grinde,B. (1998) A common RNA motif in the 30 end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J. Gen. Virol., 79(Pt 4), 715-718.
    • (1998) J. Gen. Virol , vol.79 , Issue.PART 4 , pp. 715-718
    • Jonassen, C.M.1    Jonassen, T.O.2    Grinde, B.3
  • 49
    • 0347634413 scopus 로고    scopus 로고
    • A cis-acting replication element in the sequence encoding the nS5B RNA-dependent RNA polymerase is required for hepatitis c virus RNA replication
    • You,S., Stump,D.D., Branch,A.D. and Rice,C.M. (2004) A cis-acting replication element in the sequence encoding the nS5B RNA-dependent RNA polymerase is required for hepatitis c virus RNA replication. J. Virol., 78, 1352-1366.
    • (2004) J. Virol , vol.78 , pp. 1352-1366
    • You, S.1    Stump, D.D.2    Branch, A.D.3    Rice, C.M.4
  • 50
    • 0034751118 scopus 로고    scopus 로고
    • Cis-acting sequences required for coronavirus infectious bronchitis virus defective-RNA replication and packaging
    • Dalton,K., Casais,R., Shaw,K., Stirrups,K., Evans,S., Britton,P., Brown,T.D. and Cavanagh,D. (2001) Cis-acting sequences required for coronavirus infectious bronchitis virus defective-RNA replication and packaging. J. Virol., 75, 125-133.
    • (2001) J. Virol , vol.75 , pp. 125-133
    • Dalton, K.1    Casais, R.2    Shaw, K.3    Stirrups, K.4    Evans, S.5    Britton, P.6    Brown, T.D.7    Cavanagh, D.8
  • 51
    • 3142655975 scopus 로고    scopus 로고
    • Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus
    • McCormack,J.C. and Simon,A.E. (2004) Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus. J. Virol. 78(14), 7813-7817.
    • (2004) J. Virol , vol.78 , Issue.14 , pp. 7813-7817
    • McCormack, J.C.1    Simon, A.E.2
  • 52
    • 0032540161 scopus 로고    scopus 로고
    • Differentially expressed snoRNAs in Bungarus multicinctus (Taiwan banded krait)
    • Chang,L.S., Lin,S.K. and Wu, P.F. (1998) Differentially expressed snoRNAs in Bungarus multicinctus (Taiwan banded krait). Biochem. Biophys. Res. Commun., 245, 397-402.
    • (1998) Biochem. Biophys. Res. Commun , vol.245 , pp. 397-402
    • Chang, L.S.1    Lin, S.K.2    Wu, P.F.3
  • 53
    • 2942718696 scopus 로고    scopus 로고
    • Human box h/aca pseudouridylation guide RNA machinery
    • Kiss,A.M., Jdy,B.E., Bertrand,E. and Kiss,T. (2004) Human box h/aca pseudouridylation guide RNA machinery. Mol. Cell. Biol., 24, 5797-5807.
    • (2004) Mol. Cell. Biol , vol.24 , pp. 5797-5807
    • Kiss, A.M.1    Jdy, B.E.2    Bertrand, E.3    Kiss, T.4
  • 54
    • 0037102582 scopus 로고    scopus 로고
    • RNA molecules with structure dependent functions are uniquely folded
    • Le,S.Y., Zhang,K. and Maizel,J.V.J. (2002) RNA molecules with structure dependent functions are uniquely folded. Nucleic Acids Res., 30 3574-2582.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3574-2582
    • Le, S.Y.1    Zhang, K.2    Maizel, J.V.J.3
  • 55
    • 0035836340 scopus 로고    scopus 로고
    • Features of the 30-consensus sequence of rotavirus mRNAs critical to minus strand synthesis
    • Chen,D., Barros,M., Spencer,E. and Patton,J.T. (2001) Features of the 30-consensus sequence of rotavirus mRNAs critical to minus strand synthesis. Virology, 282, 221-229.
    • (2001) Virology , vol.282 , pp. 221-229
    • Chen, D.1    Barros, M.2    Spencer, E.3    Patton, J.T.4
  • 56
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • Walter,A., Turner,D., Kim,J., Lyttle,M., Muller,P., Mathews,D. and Zuker,M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA, 91, 9218-9222.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 9218-9222
    • Walter, A.1    Turner, D.2    Kim, J.3    Lyttle, M.4    Muller, P.5    Mathews, D.6    Zuker, M.7
  • 57
    • 0035368207 scopus 로고    scopus 로고
    • The ins and outs of group II introns
    • Bonen, L. and Vogel, J. (2001) The ins and outs of group II introns. Trends Genet., 17, 322-331.
    • (2001) Trends Genet , vol.17 , pp. 322-331
    • Bonen, L.1    Vogel, J.2


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