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Volumn 14, Issue 1, 2013, Pages

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

BASE-PAIRING RULES; MUTUAL INFORMATIONS; PHYLOGENETIC INFORMATION; PHYLOGENETIC TREES; SCORING SCHEMES; STRUCTURE DETECTION; STRUCTURE PREDICTION; THERMODYNAMIC MODEL;

EID: 84876670684     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-142     Document Type: Article
Times cited : (6)

References (51)
  • 1
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • 10.1038/35103511, 11733745
    • Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2(12):919-929. 10.1038/35103511, 11733745.
    • (2001) Nat Rev Genet , vol.2 , Issue.12 , pp. 919-929
    • Eddy, S.R.1
  • 2
    • 0141867857 scopus 로고    scopus 로고
    • Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
    • 10.1002/bies.10332, 14505360
    • Mattick JS. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 2003, 25(10):930-939. 10.1002/bies.10332, 14505360.
    • (2003) Bioessays , vol.25 , Issue.10 , pp. 930-939
    • Mattick, J.S.1
  • 3
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: small RNAs with a big role in gene regulation
    • 10.1038/nrg1379, 15211354
    • He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004, 5(7):522-531. 10.1038/nrg1379, 15211354.
    • (2004) Nat Rev Genet , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 4
    • 2942560804 scopus 로고    scopus 로고
    • Gene regulation by riboswitches
    • 10.1038/nrm1403, 15173824
    • Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 2004, 5(6):451-463. 10.1038/nrm1403, 15173824.
    • (2004) Nat Rev Mol Cell Biol , vol.5 , Issue.6 , pp. 451-463
    • Mandal, M.1    Breaker, R.R.2
  • 5
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project C., 10.1038/nature11247, 3439153, 22955616
    • The ENCODE Project C. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489(7414):57-74. 10.1038/nature11247, 3439153, 22955616.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 6
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • The FANTOM Consortium
    • The FANTOM Consortium The transcriptional landscape of the mammalian genome. Science 2005, 309(5740):1559-1563. The FANTOM Consortium.
    • (2005) Science , vol.309 , Issue.5740 , pp. 1559-1563
  • 7
    • 33645294070 scopus 로고    scopus 로고
    • Oncomirs - microRNAs with a role in cancer
    • Esquela-Kerscher A, Slack FJ. Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 2006, 6(4):259-269.
    • (2006) Nat Rev Cancer , vol.6 , Issue.4 , pp. 259-269
    • Esquela-Kerscher, A.1    Slack, F.J.2
  • 8
    • 70349320158 scopus 로고    scopus 로고
    • Causes and consequences of microRNA dysregulation in cancer
    • 10.1038/nrg2634, 3467096, 19763153
    • Croce CM. Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 2009, 10(10):704-714. 10.1038/nrg2634, 3467096, 19763153.
    • (2009) Nat Rev Genet , vol.10 , Issue.10 , pp. 704-714
    • Croce, C.M.1
  • 10
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs insights into functions
    • 10.1038/nrg2521, 19188922
    • Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs insights into functions. Nat Rev Genet 2009, 10(3):155-159. 10.1038/nrg2521, 19188922.
    • (2009) Nat Rev Genet , vol.10 , Issue.3 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 11
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • 10.1093/nar/9.1.133, 326673, 6163133
    • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981, 9:133-148. 10.1093/nar/9.1.133, 326673, 6163133.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 13
    • 0345005029 scopus 로고
    • Improved predictions of secondary structures for RNA
    • 10.1073/pnas.86.20.7706, 298139, 2479010
    • Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 1989, 86(20):7706-7710. 10.1073/pnas.86.20.7706, 298139, 2479010.
    • (1989) Proc Natl Acad Sci USA , vol.86 , Issue.20 , pp. 7706-7710
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 14
    • 0033572893 scopus 로고    scopus 로고
    • No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    • 10.1093/nar/27.24.4816, 148783, 10572183
    • Workman C, Krogh A. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 1999, 27(24):4816-4822. 10.1093/nar/27.24.4816, 148783, 10572183.
    • (1999) Nucleic Acids Res , vol.27 , Issue.24 , pp. 4816-4822
    • Workman, C.1    Krogh, A.2
  • 15
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • 10.1093/bioinformatics/16.7.583, 11038329
    • Rivas E, Eddy SR. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 2000, 16(7):583-605. 10.1093/bioinformatics/16.7.583, 11038329.
    • (2000) Bioinformatics , vol.16 , Issue.7 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 16
    • 0002277269 scopus 로고
    • 4 Probing RNA structure, function, and history by comparative analysis
    • Woese CR, Pace NR. 4 Probing RNA structure, function, and history by comparative analysis. Cold Spring Harbor Monograph Archive 1993, 24:91-117.
    • (1993) Cold Spring Harbor Monograph Archive , vol.24 , pp. 91-117
    • Woese, C.R.1    Pace, N.R.2
  • 17
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J Appl Math 1985, 45(5):810-825.
    • (1985) SIAM J Appl Math , vol.45 , Issue.5 , pp. 810-825
    • Sankoff, D.1
  • 18
    • 34248632816 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
    • 10.1186/1471-2105-8-130, 1868766, 17445273
    • Harmanci AO, Sharma G, Mathews DH. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics 2007, 8:130. 10.1186/1471-2105-8-130, 1868766, 17445273.
    • (2007) BMC Bioinformatics , vol.8 , pp. 130
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 19
    • 35748971022 scopus 로고    scopus 로고
    • Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
    • 2014794, 17937495
    • Havgaard JH, Torarinsson E, Gorodkin J. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol 2007, 3(10):1896-1908. 2014794, 17937495.
    • (2007) PLoS Comput Biol , vol.3 , Issue.10 , pp. 1896-1908
    • Havgaard, J.H.1    Torarinsson, E.2    Gorodkin, J.3
  • 20
    • 34247598415 scopus 로고    scopus 로고
    • Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
    • 10.1371/journal.pcbi.0030065, 1851984, 17432929
    • Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007, 3(4):e65. 10.1371/journal.pcbi.0030065, 1851984, 17432929.
    • (2007) PLoS Comput Biol , vol.3 , Issue.4
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 21
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • 10.1186/1471-2105-7-400, 1579236, 16952317
    • Dowell RD, Eddy SR. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 2006, 7:400. 10.1186/1471-2105-7-400, 1579236, 16952317.
    • (2006) BMC Bioinformatics , vol.7 , pp. 400
    • Dowell, R.D.1    Eddy, S.R.2
  • 22
    • 0025832114 scopus 로고
    • Inferring consensus structure from nucleic acid sequences
    • Chiu DKY, Kolodziejczak T. Inferring consensus structure from nucleic acid sequences. Comput Appl Biosci : CABIOS 1991, 7(3):347-352.
    • (1991) Comput Appl Biosci : CABIOS , vol.7 , Issue.3 , pp. 347-352
    • Chiu, D.K.Y.1    Kolodziejczak, T.2
  • 23
    • 0025191217 scopus 로고
    • Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs
    • 10.1073/pnas.87.2.663, 53325, 2300554
    • Gutell RR, Woese CR. Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs. Proc Natl Acad Sci USA 1990, 87(2):663-667. 10.1073/pnas.87.2.663, 53325, 2300554.
    • (1990) Proc Natl Acad Sci USA , vol.87 , Issue.2 , pp. 663-667
    • Gutell, R.R.1    Woese, C.R.2
  • 24
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods
    • 10.1093/nar/20.21.5785, 334417, 1454539
    • Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 1992, 20(21):5785-5795. 10.1093/nar/20.21.5785, 334417, 1454539.
    • (1992) Nucleic Acids Res , vol.20 , Issue.21 , pp. 5785-5795
    • Gutell, R.R.1    Power, A.2    Hertz, G.Z.3    Putz, E.J.4    Stormo, G.D.5
  • 25
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • 10.1016/S0022-2836(02)00308-X, 12079347
    • Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol 2002, 319(5):1059-1066. 10.1016/S0022-2836(02)00308-X, 12079347.
    • (2002) J Mol Biol , vol.319 , Issue.5 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 26
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • 10.1093/nar/22.11.2079, 308124, 8029015
    • Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res 1994, 22(11):2079-2088. 10.1093/nar/22.11.2079, 308124, 8029015.
    • (1994) Nucleic Acids Res , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 29
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • 10.1093/bioinformatics/15.6.446, 10383470
    • Knudsen B, Hein J. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15(6):446-454. 10.1093/bioinformatics/15.6.446, 10383470.
    • (1999) Bioinformatics , vol.15 , Issue.6 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 30
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • 10.1093/nar/gkg614, 169020, 12824339
    • Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 2003, 31(13):3423-3428. 10.1093/nar/gkg614, 169020, 12824339.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 31
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • 10.1093/bioinformatics/btl246, 16873527
    • Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006, 22(14):e90-e98. 10.1093/bioinformatics/btl246, 16873527.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 32
    • 56649099274 scopus 로고    scopus 로고
    • Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
    • 10.1093/nar/gkn544, 2582601, 18836192
    • Seemann SE, Gorodkin J, Backofen R. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res 2008, 36(20):6355-6362. 10.1093/nar/gkn544, 2582601, 18836192.
    • (2008) Nucleic Acids Res , vol.36 , Issue.20 , pp. 6355-6362
    • Seemann, S.E.1    Gorodkin, J.2    Backofen, R.3
  • 34
    • 58249121729 scopus 로고    scopus 로고
    • RNAalifold: improved consensus structure prediction for RNA alignments
    • 10.1186/1471-2105-9-474, 2621365, 19014431
    • Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 2008, 9:474. 10.1186/1471-2105-9-474, 2621365, 19014431.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474
    • Bernhart, S.H.1    Hofacker, I.L.2    Will, S.3    Gruber, A.R.4    Stadler, P.F.5
  • 35
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • 10.1126/science.2468181, 2468181
    • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 1989, 244(4900):48-52. 10.1126/science.2468181, 2468181.
    • (1989) Science , vol.244 , Issue.4900 , pp. 48-52
    • Zuker, M.1
  • 38
    • 4143149651 scopus 로고    scopus 로고
    • Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
    • 10.1016/j.jmb.2004.07.018, 15313604
    • Washietl S, Hofacker IL. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 2004, 342:19-30. 10.1016/j.jmb.2004.07.018, 15313604.
    • (2004) J Mol Biol , vol.342 , pp. 19-30
    • Washietl, S.1    Hofacker, I.L.2
  • 39
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • 10.1126/science.155.3760.279, 5334057
    • Fitch WM, Margoliash E. Construction of phylogenetic trees. Science 1967, 155(3760):279-284. 10.1126/science.155.3760.279, 5334057.
    • (1967) Science , vol.155 , Issue.3760 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 41
    • 60849086186 scopus 로고    scopus 로고
    • Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA
    • 10.1186/1471-2105-10-S1-S37, 2648794, 19208138
    • Xia F, Dou Y, Zhou X, Yang X, Xu J, Zhang Y. Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA. BMC Bioinformatics 2009, 10(Suppl 1):S37. 10.1186/1471-2105-10-S1-S37, 2648794, 19208138.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 1
    • Xia, F.1    Dou, Y.2    Zhou, X.3    Yang, X.4    Xu, J.5    Zhang, Y.6
  • 43
    • 32544452741 scopus 로고    scopus 로고
    • CMfinder-a covariance model based RNA motif finding algorithm
    • 10.1093/bioinformatics/btk008, 16357030
    • Yao Z, Weinberg Z, Ruzzo WL. CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22(4):445-452. 10.1093/bioinformatics/btk008, 16357030.
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 445-452
    • Yao, Z.1    Weinberg, Z.2    Ruzzo, W.L.3
  • 45
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version 3.2)
    • Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 46
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • 10.1186/1471-2105-5-140, 526219, 15458580
    • Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004, 5:140. 10.1186/1471-2105-5-140, 526219, 15458580.
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 47
    • 2942544566 scopus 로고    scopus 로고
    • RSEARCH: finding homologs of single structured RNA sequences
    • 10.1186/1471-2105-4-44, 239859, 14499004
    • Klein RJ, Eddy SR. RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 2003, 4:44. 10.1186/1471-2105-4-44, 239859, 14499004.
    • (2003) BMC Bioinformatics , vol.4 , pp. 44
    • Klein, R.J.1    Eddy, S.R.2
  • 48
    • 79959930135 scopus 로고    scopus 로고
    • The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
    • 3125731, 21609960
    • Seemann SE, Menzel P, Backofen R, Gorodkin J. The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. Nucleic Acids Res 2011, 39(Web Server issue):W107-W111. 3125731, 21609960.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE
    • Seemann, S.E.1    Menzel, P.2    Backofen, R.3    Gorodkin, J.4
  • 49
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal RR, Michener CD. A statistical method for evaluating systematic relationships. University Kansas Scienti Bull 1958, 28:1409-1438.
    • (1958) University Kansas Scienti Bull , vol.28 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 51
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • 10.1093/bioinformatics/17.8.754, 11524383
    • Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17(8):754-755. 10.1093/bioinformatics/17.8.754, 11524383.
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2


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