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Volumn 22, Issue 24, 2006, Pages 2988-2995

Measuring covariation in RNA alignments: Physical realism improves information measures

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

EID: 33845362968     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl514     Document Type: Article
Times cited : (50)

References (41)
  • 1
    • 0033832578 scopus 로고    scopus 로고
    • Phylogenetically enhanced statistical tools for RNA structure prediction
    • Akmaev, V.R. et al. (2000) Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics, 16, 501-512.
    • (2000) Bioinformatics , vol.16 , pp. 501-512
    • Akmaev, V.R.1
  • 2
    • 33344469705 scopus 로고    scopus 로고
    • RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
    • Bindewald,E. and Shapiro,B. (2006) RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA, 12, 342-352.
    • (2006) RNA , vol.12 , pp. 342-352
    • Bindewald, E.1    Shapiro, B.2
  • 3
    • 0016189342 scopus 로고
    • Stability of ribonucleic acid double-stranded helices
    • Borer,P. et al. (1974) Stability of ribonucleic acid double-stranded helices. J. Mol. Evol., 86, 843-853.
    • (1974) J. Mol. Evol. , vol.86 , pp. 843-853
    • Borer, P.1
  • 4
    • 0025832114 scopus 로고
    • Inferring consensus structure from nucleic acid sequences
    • Chiu,D.K. and Kolodziejczak,T. (1991) Inferring consensus structure from nucleic acid sequences. Comput. Appl. Biosci., 7, 347-352.
    • (1991) Comput. Appl. Biosci. , vol.7 , pp. 347-352
    • Chiu, D.K.1    Kolodziejczak, T.2
  • 5
    • 4344584927 scopus 로고    scopus 로고
    • MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
    • Coventry,A. et al. (2004) MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure. Proc. Natl. Acad. Sci. USA, 101, 12102-12107.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 12102-12107
    • Coventry, A.1
  • 8
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy,S. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 2079-2088
    • Eddy, S.1    Durbin, R.2
  • 9
    • 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
  • 10
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • Gardner,P. et al. (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.1
  • 11
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most significant common sequence and structure motifs in a set of RNA sequences
    • Gorodkin,J. et al. (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
  • 12
    • 0032847645 scopus 로고    scopus 로고
    • Matrixplot: Visualizing sequence constraints
    • Gorodkin,J. et al. (1999) Matrixplot: Visualizing sequence constraints. Bioinformatics, 15, 769-770.
    • (1999) Bioinformatics , vol.15 , pp. 769-770
    • Gorodkin, J.1
  • 13
    • 0037252684 scopus 로고    scopus 로고
    • Rfam: An RNA family database
    • Griffiths-Jones,S. et al. (2003) Rfam: An RNA family database. Nucleic Acids Res., 31, 439-441.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 439-441
    • Griffiths-Jones, S.1
  • 14
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
    • Gutell,R.R. et al. (1992) Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-5795.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5785-5795
    • Gutell, R.R.1
  • 15
    • 16344363338 scopus 로고    scopus 로고
    • Pairwise local structure alignment of RNA sequences with sequence similarity less than 40%
    • Havgaard,J.H. et al. (2005) Pairwise local structure alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics, 21, 1815-1824.
    • (2005) Bioinformatics , vol.21 , pp. 1815-1824
    • Havgaard, J.H.1
  • 16
    • 34249772381 scopus 로고
    • Fast folding and comparison of RNA secondary structures
    • Hofacker,I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie, 125, 167-188.
    • (1994) Monatshefte Für Chemie , vol.125 , pp. 167-188
    • Hofacker, I.L.1
  • 17
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker,I.L. et al. (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
  • 18
    • 5044242515 scopus 로고    scopus 로고
    • Alignment of RNA base pairing probability matrices
    • Hofacker,I.L. et al. (2004) Alignment of RNA base pairing probability matrices. Bioinformatics, 20, 2222-2227.
    • (2004) Bioinformatics , vol.20 , pp. 2222-2227
    • Hofacker, I.L.1
  • 19
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen,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
    • Knudsen, B.1    Hein, J.2
  • 21
  • 22
    • 9244238182 scopus 로고    scopus 로고
    • Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs
    • Lee,J. and Gutell,R. (2004) Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. J. Mol. Biol., 344, 1225-1249.
    • (2004) J. Mol. Biol. , vol.344 , pp. 1225-1249
    • Lee, J.1    Gutell, R.2
  • 23
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis,N. et al. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3497-3531
    • Leontis, N.1
  • 24
    • 0033230822 scopus 로고    scopus 로고
    • ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure
    • Lück,R. et al. (1999) ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res., 27, 4208-4217.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4208-4217
    • Lück, R.1
  • 25
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • Martin,L.C. et al. (2005) Using information theory to search for co-evolving residues in proteins. Bioinformatics, 21, 4116-4124.
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.C.1
  • 26
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews,D.H. and TurnerD.H. (2002) Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Bio., 317, 191-203.
    • (2002) J. Mol. Bio. , vol.317 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 27
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • Mathews,D.H. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA, 10, 1178-1190.
    • (2004) RNA , vol.10 , pp. 1178-1190
    • Mathews, D.H.1
  • 28
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews,D. et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7287-7292
    • Mathews, D.1
  • 29
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of 14 phage lysozyme
    • Matthews,B. (1975) Comparison of the predicted and observed secondary structure of 14 phage lysozyme. Biochimica et Biophysica Acta, 405, 442-451.
    • (1975) Biochimica Et Biophysica Acta , vol.405 , pp. 442-451
    • Matthews, B.1
  • 30
    • 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
  • 32
    • 33646272409 scopus 로고    scopus 로고
    • Identification and classification of conserved RNA secondary structures in the human genome
    • Pedersen,J. et al. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol., 2.
    • (2006) PLoS Comput Biol. , vol.2
    • Pedersen, J.1
  • 33
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Rivas,E. and Eddy,S.R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2.
    • (2001) BMC Bioinformatics , vol.2
    • Rivas, E.1    Eddy, S.R.2
  • 34
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • Ruan,J. et al. (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20, 58-66.
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1
  • 35
    • 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
  • 36
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • 379-423
    • Shannon,C.E. (1948) A mathematical theory of communication. The Bell Syst. Tech. J., 27, 379-423, 623-656.
    • (1948) The Bell Syst. Tech. J. , vol.27 , pp. 623-656
    • Shannon, C.E.1
  • 37
    • 0036084598 scopus 로고    scopus 로고
    • 5S ribosomal RNA database
    • Szymanski,M. et al. (2002) 5S ribosomal RNA database. Nucleic Acids Res., 30, 176-178.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 176-178
    • Szymanski, M.1
  • 38
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • Washietl,S. et al. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454-2459.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2454-2459
    • Washietl, S.1
  • 39
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 40
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 41
    • 0030763695 scopus 로고    scopus 로고
    • The uRNA database
    • Zwieb,C. (1997) The uRNA database. Nucleic Acids Res., 25, 102-103.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 102-103
    • Zwieb, C.1


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