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Volumn 15, Issue 5, 2013, Pages 748-767

Fighting against uncertainty: An essential issue in bioinformatics

Author keywords

Bioinformatics; Estimation problems; Sequence analysis; Uncertainty of solutions

Indexed keywords

RNA;

EID: 84921758344     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt038     Document Type: Article
Times cited : (13)

References (103)
  • 2
    • 84859898660 scopus 로고    scopus 로고
    • A beginner's guide to eukaryotic genome annotation
    • Yandell M, Ence D. A beginner's guide to eukaryotic genome annotation. Nat Rev Genet 2012;13:329-342.
    • (2012) Nat Rev Genet , vol.13 , pp. 329-342
    • Yandell, M.1    Ence, D.2
  • 3
    • 84864116955 scopus 로고    scopus 로고
    • RNA structure prediction:an overview of methods
    • Seetin MG, Mathews DH. RNA structure prediction:an overview of methods. Methods Mol Biol 2012;905(45):99-122.
    • (2012) Methods Mol Biol , vol.905 , Issue.45 , pp. 99-122
    • Seetin, M.G.1    Mathews, D.H.2
  • 5
    • 77956503102 scopus 로고    scopus 로고
    • RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
    • Kato Y, Sato K, Hamada M, et al. RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 2010;26(18):i460-i466.
    • (2010) Bioinformatics , vol.26 , Issue.18 , pp. i460-i466
    • Kato, Y.1    Sato, K.2    Hamada, M.3
  • 7
    • 84877260669 scopus 로고    scopus 로고
    • COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account
    • Proctor JR, Meyer IM. COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Res 2013;41(9):e102.
    • (2013) Nucleic Acids Res , vol.41 , Issue.9 , pp. e102
    • Proctor, J.R.1    Meyer, I.M.2
  • 8
    • 1042304206 scopus 로고    scopus 로고
    • Prediction of locally stable RNA secondary structures for genome-wide surveys
    • Hofacker IL, Priwitzer B, Stadler PF. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 2004;20(2):186-190.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 186-190
    • Hofacker, I.L.1    Priwitzer, B.2    Stadler, P.F.3
  • 9
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990; 29(6-7):1105-1119.
    • (1990) Biopolymers , vol.29 , Issue.6-7 , pp. 1105-1119
    • McCaskill, J.S.1
  • 10
    • 79953154800 scopus 로고    scopus 로고
    • Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction
    • Barash D, Churkin A. Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. Brief Bioinformatics 2011;12(2):104-114.
    • (2011) Brief Bioinformatics , vol.12 , Issue.2 , pp. 104-114
    • Barash, D.1    Churkin, A.2
  • 11
    • 33745873714 scopus 로고    scopus 로고
    • RNAmute: RNA secondary structure mutation analysis tool
    • Churkin A, Barash D. RNAmute: RNA secondary structure mutation analysis tool. BMC Bioinformatics 2006; 7:221.
    • (2006) BMC Bioinformatics , vol.7 , pp. 221
    • Churkin, A.1    Barash, D.2
  • 12
    • 50949133711 scopus 로고    scopus 로고
    • Efficient algorithms for probing the RNA mutation landscape
    • Waldispuhl J, Devadas S, Berger B, et al. Efficient algorithms for probing the RNA mutation landscape. PLoSComput Biol 2008;4(8):e1000124.
    • (2008) PLoSComput Biol , vol.4 , Issue.8 , pp. e1000124
    • Waldispuhl, J.1    Devadas, S.2    Berger, B.3
  • 13
    • 39049145326 scopus 로고    scopus 로고
    • Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    • Lunter G, Rocco A, Mimouni N, et al. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. GenomeRes 2008;18(2):298-309.
    • (2008) GenomeRes , vol.18 , Issue.2 , pp. 298-309
    • Lunter, G.1    Rocco, A.2    Mimouni, N.3
  • 14
    • 84870787518 scopus 로고    scopus 로고
    • Informationtheoretic uncertainty of SCFG-modeled folding space of the non-coding RNA
    • Manzourolajdad A, Wang Y, Shaw TI, et al. Informationtheoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. JTheor Biol 2012;318C:140-163.
    • (2012) JTheor Biol , vol.318 , Issue.C , pp. 140-163
    • Manzourolajdad, A.1    Wang, Y.2    Shaw, T.I.3
  • 15
    • 38549135938 scopus 로고    scopus 로고
    • Alignment uncertainty and genomic analysis
    • Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science 2008;319(5862):473-476.
    • (2008) Science , vol.319 , Issue.5862 , pp. 473-476
    • Wong, K.M.1    Suchard, M.A.2    Huelsenbeck, J.P.3
  • 16
    • 77957233773 scopus 로고    scopus 로고
    • The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection
    • Fletcher W, Yang Z. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 2010;27(10):2257-2267.
    • (2010) Mol Biol Evol , vol.27 , Issue.10 , pp. 2257-2267
    • Fletcher, W.1    Yang, Z.2
  • 17
    • 79953072316 scopus 로고    scopus 로고
    • Parametric analysis of alignment and phylogenetic uncertainty
    • Malaspinas AS, Eriksson N, Huggins P. Parametric analysis of alignment and phylogenetic uncertainty. Bull Math Biol 2011;73(4):795-810.
    • (2011) Bull Math Biol , vol.73 , Issue.4 , pp. 795-810
    • Malaspinas, A.S.1    Eriksson, N.2    Huggins, P.3
  • 19
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 1989;244:48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 20
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003;31(13):3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 21
    • 0033563515 scopus 로고    scopus 로고
    • A bayesian statistical algorithm for RNA secondary structure prediction
    • Ding Y, Lawrence CE. A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem 1999; 23(3-4):387-400.
    • (1999) Comput Chem , vol.23 , Issue.3-4 , pp. 387-400
    • Ding, Y.1    Lawrence, C.E.2
  • 22
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty S, Fontana W, Hofacker IL, et al. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999;49(2):145-165.
    • (1999) Biopolymers , vol.49 , Issue.2 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3
  • 23
    • 84972511893 scopus 로고
    • Practical Markov Chain Monte Carlo
    • Geyer CJ. Practical Markov Chain Monte Carlo. Stat Sci 1992;7(4):473-483.
    • (1992) Stat Sci , vol.7 , Issue.4 , pp. 473-483
    • Geyer, C.J.1
  • 24
    • 34548443728 scopus 로고    scopus 로고
    • SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
    • Meyer IM, Miklos I. SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol 2007;3(8):e149.
    • (2007) PLoS Comput Biol , vol.3 , Issue.8 , pp. e149
    • Meyer, I.M.1    Miklos, I.2
  • 25
    • 36448984918 scopus 로고    scopus 로고
    • Predicting RNA secondary structures with pseudoknots by MCMC sampling
    • Metzler D, Nebel ME. Predicting RNA secondary structures with pseudoknots by MCMC sampling. J Math Biol 2008; 56(1-2):161-181.
    • (2008) J Math Biol , vol.56 , Issue.1-2 , pp. 161-181
    • Metzler, D.1    Nebel, M.E.2
  • 26
    • 84873654239 scopus 로고    scopus 로고
    • McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
    • Bon M, Micheletti C, Orland H. McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots. Nucleic Acids Res 2013;41(3):1895-1900.
    • (2013) Nucleic Acids Res , vol.41 , Issue.3 , pp. 1895-1900
    • Bon, M.1    Micheletti, C.2    Orland, H.3
  • 27
    • 80053123373 scopus 로고    scopus 로고
    • Counting RNA pseudoknotted structures
    • Saule C, Regnier M, Steyaert JM, et al. Counting RNA pseudoknotted structures. J Comput Biol 2011;18(10):1339-1351.
    • (2011) J Comput Biol , vol.18 , Issue.10 , pp. 1339-1351
    • Saule, C.1    Regnier, M.2    Steyaert, J.M.3
  • 28
    • 84865546962 scopus 로고    scopus 로고
    • Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots
    • Doose G, Metzler D. Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots. Bioinformatics 2012;28(17):2242-2248.
    • (2012) Bioinformatics , vol.28 , Issue.17 , pp. 2242-2248
    • Doose, G.1    Metzler, D.2
  • 29
    • 80052736874 scopus 로고    scopus 로고
    • RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences
    • Wei D, Alpert LV, Lawrence CE. RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics 2011;27(18):2486-2493.
    • (2011) Bioinformatics , vol.27 , Issue.18 , pp. 2486-2493
    • Wei, D.1    Alpert, L.V.2    Lawrence, C.E.3
  • 30
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001;17(8):754-755.
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 31
    • 70349205853 scopus 로고    scopus 로고
    • BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
    • Satija R, Novak A, Miklos I, et al. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol Biol 2009;9:217.
    • (2009) BMC Evol Biol , vol.9 , pp. 217
    • Satija, R.1    Novak, A.2    Miklos, I.3
  • 32
    • 13444292041 scopus 로고    scopus 로고
    • An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model
    • Clote P. An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J Comput Biol 2005; 12(1):83-101.
    • (2005) J Comput Biol , vol.12 , Issue.1 , pp. 83-101
    • Clote, P.1
  • 33
    • 84867513255 scopus 로고    scopus 로고
    • RNA locally optimal secondary structures
    • Saffarian A, Giraud M, Monte de A, et al. RNA locally optimal secondary structures. J Comput Biol 2012;19(10):1120-1133.
    • (2012) J Comput Biol , vol.19 , Issue.10 , pp. 1120-1133
    • Saffarian, A.1    Giraud, M.2    Monte de, A.3
  • 34
    • 32544440797 scopus 로고    scopus 로고
    • RNAshapes: an integrated RNA analysis package based on abstract shapes
    • Steffen P, Voss B, Rehmsmeier M, et al. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 2006;22(4):500-503.
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 500-503
    • Steffen, P.1    Voss, B.2    Rehmsmeier, M.3
  • 36
    • 33745087121 scopus 로고    scopus 로고
    • Complete probabilistic analysis of RNA shapes
    • Voss B, Giegerich R, Rehmsmeier M. Complete probabilistic analysis of RNA shapes. BMC Biol 2006;4:5.
    • (2006) BMC Biol , vol.4 , pp. 5
    • Voss, B.1    Giegerich, R.2    Rehmsmeier, M.3
  • 37
    • 23644448438 scopus 로고    scopus 로고
    • RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
    • Ding Y, Chan CY, Lawrence CE. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 2005;11(8):1157-1166.
    • (2005) RNA , vol.11 , Issue.8 , pp. 1157-1166
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 38
    • 67849086863 scopus 로고    scopus 로고
    • CENTROIDFOLD: a web server for RNA secondary structure prediction
    • Sato K, Hamada M, Asai K, et al. CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res 2009;37:W277-W280.
    • (2009) Nucleic Acids Res , vol.37 , pp. W277-W280
    • Sato, K.1    Hamada, M.2    Asai, K.3
  • 41
    • 22844442543 scopus 로고    scopus 로고
    • Analysis and visualization of tree space
    • Hillis DM, Heath TA, St John K. Analysis and visualization of tree space. Syst Biol 2005;54(3):471-482.
    • (2005) Syst Biol , vol.54 , Issue.3 , pp. 471-482
    • Hillis, D.M.1    Heath, T.A.2    St John, K.3
  • 42
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D, Foulds L. Comparison of phylogenetic trees. Math Biosci 1981; 53(1-2):131-147.
    • (1981) Math Biosci , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.1    Foulds, L.2
  • 43
    • 84872078254 scopus 로고    scopus 로고
    • MASTtreedist: visualization of tree space based on maximum agreement subtree
    • Huang H, Li Y. MASTtreedist: visualization of tree space based on maximum agreement subtree. JComputBiol 2013; 20(1):42-49.
    • (2013) JComputBiol , vol.20 , Issue.1 , pp. 42-49
    • Huang, H.1    Li, Y.2
  • 44
    • 84928190496 scopus 로고    scopus 로고
    • Building Trees, Hunting for Trees, and Comparing Trees - Theory and Methods in Phylogenetic Analysis
    • PhD diss., University of Canterbury, Christchurch, New Zealand
    • David B. Building Trees, Hunting for Trees, and Comparing Trees - Theory and Methods in Phylogenetic Analysis. PhD diss., University of Canterbury, Christchurch, New Zealand, 1997.
    • (1997)
    • David, B.1
  • 45
    • 58149236993 scopus 로고    scopus 로고
    • Exact calculation of distributions on integers, with application to sequence alignment
    • Newberg LA, Lawrence CE. Exact calculation of distributions on integers, with application to sequence alignment. JComputBiol 2009;16(1):1-18.
    • (2009) JComputBiol , vol.16 , Issue.1 , pp. 1-18
    • Newberg, L.A.1    Lawrence, C.E.2
  • 46
    • 34547566768 scopus 로고    scopus 로고
    • RNAbor: a web server for RNA structural neighbors
    • Freyhult E, Moulton V, Clote P. RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res 2007;35:W305-W309.
    • (2007) Nucleic Acids Res , vol.35 , pp. W305-W309
    • Freyhult, E.1    Moulton, V.2    Clote, P.3
  • 47
    • 34548604264 scopus 로고    scopus 로고
    • Boltzmann probability of RNA structural neighbors and riboswitch detection
    • Freyhult E, Moulton V, Clote P. Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics 2007;23(16):2054-2062.
    • (2007) Bioinformatics , vol.23 , Issue.16 , pp. 2054-2062
    • Freyhult, E.1    Moulton, V.2    Clote, P.3
  • 48
    • 84867666678 scopus 로고    scopus 로고
    • Maximum expected accuracy structural neighbors of an RNA secondary structure
    • Clote P, Lou F, Lorenz WA. Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics 2012; 13(Suppl 5):S6. 2012.
    • (2012) BMC Bioinformatics , vol.13 , pp. S6
    • Clote, P.1    Lou, F.2    Lorenz, W.A.3
  • 49
    • 79954633094 scopus 로고    scopus 로고
    • 2d projections of rna folding landscapes. In: Grosse I, Neumann S, Posch S, et al (eds)
    • of LNI. GI
    • Lorenz R, Flamm C, Hofacker IL. 2d projections of rna folding landscapes. In: Grosse I, Neumann S, Posch S, et al (eds). GCB. volume 157 of LNI. GI, 2009, 11-20.
    • (2009) GCB , vol.157 , pp. 11-20
    • Lorenz, R.1    Flamm, C.2    Hofacker, I.L.3
  • 51
    • 84875475826 scopus 로고    scopus 로고
    • Visualizing RNA base-pairing probabilities with RNAbow diagrams
    • Aalberts DP, Jannen WK. Visualizing RNA base-pairing probabilities with RNAbow diagrams. RNA 2013;19:475.
    • (2013) RNA , vol.19 , pp. 475
    • Aalberts, D.P.1    Jannen, W.K.2
  • 52
    • 79958026711 scopus 로고    scopus 로고
    • Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F
    • Adachi H, Ishiguro A, Hamada M, et al. Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F. Biochimie 2011;93(7):1081-1088.
    • (2011) Biochimie , vol.93 , Issue.7 , pp. 1081-1088
    • Adachi, H.1    Ishiguro, A.2    Hamada, M.3
  • 53
    • 0029595355 scopus 로고
    • A reliable sequence alignment method based on probabilities of residue correspondences
    • Miyazawa S. A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng 1995;8(10):999-1009.
    • (1995) Protein Eng , vol.8 , Issue.10 , pp. 999-1009
    • Miyazawa, S.1
  • 54
    • 77958057991 scopus 로고    scopus 로고
    • An intuitive, informative, and most balanced representation of phylogenetic topologies
    • Iwasaki W, Takagi T. An intuitive, informative, and most balanced representation of phylogenetic topologies. Syst Biol 2010;59(5):584-593.
    • (2010) Syst Biol , vol.59 , Issue.5 , pp. 584-593
    • Iwasaki, W.1    Takagi, T.2
  • 55
    • 42149083815 scopus 로고    scopus 로고
    • Centroid estimation in discrete high-dimensional spaces with applications in biology
    • Carvalho LE, Lawrence CE. Centroid estimation in discrete high-dimensional spaces with applications in biology. Proc Natl Acad SciUSA 2008;105(9):3209-3214.
    • (2008) Proc Natl Acad SciUSA , vol.105 , Issue.9 , pp. 3209-3214
    • Carvalho, L.E.1    Lawrence, C.E.2
  • 56
    • 79951974555 scopus 로고    scopus 로고
    • Generalized centroid estimators in bioinformatics
    • Hamada M, Kiryu H, Iwasaki W, et al. Generalized centroid estimators in bioinformatics. PLoS One 2011;6(2):e16450.
    • (2011) PLoS One , vol.6 , Issue.2 , pp. e16450
    • Hamada, M.1    Kiryu, H.2    Iwasaki, W.3
  • 57
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006;22(14):e90-e98.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. e90-e98
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 58
    • 60149094002 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure using generalized centroid estimators
    • Hamada M, Kiryu H, Sato K, et al. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 2009;25(4):465-473.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 465-473
    • Hamada, M.1    Kiryu, H.2    Sato, K.3
  • 59
    • 84860704698 scopus 로고    scopus 로고
    • A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA)
    • Hamada M, Asai K. A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). JComputBiol 2012;19(5):532-549.
    • (2012) JComputBiol , vol.19 , Issue.5 , pp. 532-549
    • Hamada, M.1    Asai, K.2
  • 60
    • 78649469968 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
    • Hamada M, Sato K, Asai K. Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics 2010;11:586.
    • (2010) BMC Bioinformatics , vol.11 , pp. 586
    • Hamada, M.1    Sato, K.2    Asai, K.3
  • 62
    • 0036733640 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic protein- coding genes
    • Zhang MQ. Computational prediction of eukaryotic protein- coding genes. Nat Rev Genet 2002;3(9):698-709.
    • (2002) Nat Rev Genet , vol.3 , Issue.9 , pp. 698-709
    • Zhang, M.Q.1
  • 63
    • 40449115745 scopus 로고    scopus 로고
    • CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    • Gross SS, Do CB, Sirota M, et al. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 2007;8(12):R269.
    • (2007) Genome Biol , vol.8 , Issue.12 , pp. R269
    • Gross, S.S.1    Do, C.B.2    Sirota, M.3
  • 66
    • 80055096207 scopus 로고    scopus 로고
    • PSAR: measuring multiple sequence alignment reliability by probabilistic sampling
    • Kim J, Ma J. PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Res 2011;39(15):6359-6368.
    • (2011) Nucleic Acids Res , vol.39 , Issue.15 , pp. 6359-6368
    • Kim, J.1    Ma, J.2
  • 67
    • 44949258055 scopus 로고    scopus 로고
    • Measuring global credibility with application to local sequence alignment
    • Webb-Robertson BJ, McCue LA, Lawrence CE. Measuring global credibility with application to local sequence alignment. PLoSComput Biol 2008;4(5):e1000077.
    • (2008) PLoSComput Biol , vol.4 , Issue.5 , pp. e1000077
    • Webb-Robertson, B.J.1    McCue, L.A.2    Lawrence, C.E.3
  • 68
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30:772-780.
    • (2013) Mol Biol Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 69
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res 1994;22(11):2079-2088.
    • (1994) Nucleic Acids Res , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 70
    • 75849160582 scopus 로고    scopus 로고
    • CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
    • Hamada M, Sato K, Kiryu H, et al. CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 2009;25(24):3236-3243.
    • (2009) Bioinformatics , vol.25 , Issue.24 , pp. 3236-3243
    • Hamada, M.1    Sato, K.2    Kiryu, H.3
  • 71
    • 34247598415 scopus 로고    scopus 로고
    • Inferring noncoding RNA families and classes by means of genome-scale structure- based clustering
    • Will S, Reiche K, Hofacker IL, et al. Inferring noncoding RNA families and classes by means of genome-scale structure- based clustering. PLoSComput Biol 2007;3(4):e65.
    • (2007) PLoSComput Biol , vol.3 , Issue.4 , pp. e65
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3
  • 72
    • 79551480068 scopus 로고    scopus 로고
    • Improving the accuracy of predicting secondary structure for aligned RNA sequences
    • Hamada M, Sato K, Asai K. Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res 2011;39(2):393-402.
    • (2011) Nucleic Acids Res , vol.39 , Issue.2 , pp. 393-402
    • Hamada, M.1    Sato, K.2    Asai, K.3
  • 73
    • 58249121729 scopus 로고    scopus 로고
    • RNAalifold: improved consensus structure prediction for RNA alignments
    • Bernhart SH, Hofacker IL, Will S, et al. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 2008;9:474.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474
    • Bernhart, S.H.1    Hofacker, I.L.2    Will, S.3
  • 74
    • 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. SIAMJApplMath 1985;45:810-825.
    • (1985) SIAMJApplMath , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 75
    • 66349124254 scopus 로고    scopus 로고
    • Predictions of RNA secondary structure by combining homologous sequence information
    • Hamada M, Sato K, Kiryu H, et al. Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 2009;25(12):i330-i338.
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. i330-i338
    • Hamada, M.1    Sato, K.2    Kiryu, H.3
  • 76
    • 80053194792 scopus 로고    scopus 로고
    • Base-calling for next-generation sequencing platforms
    • Ledergerber C, Dessimoz C. Base-calling for next-generation sequencing platforms. Brief Bioinformatics 2011;12(5):489-497.
    • (2011) Brief Bioinformatics , vol.12 , Issue.5 , pp. 489-497
    • Ledergerber, C.1    Dessimoz, C.2
  • 77
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25(14):1754-1760.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 78
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. NatMethods 2012;9(4):357-359.
    • (2012) NatMethods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 79
    • 84876249593 scopus 로고    scopus 로고
    • An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome
    • Shrestha AM, Frith MC. An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome. Bioinformatics 2013;29(8):965-972.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 965-972
    • Shrestha, A.M.1    Frith, M.C.2
  • 80
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25(16):2078-2079.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 81
    • 84863229597 scopus 로고    scopus 로고
    • VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. GenomeRes 2012;22(3):568-576.
    • (2012) GenomeRes , vol.22 , Issue.3 , pp. 568-576
    • Koboldt, D.C.1    Zhang, Q.2    Larson, D.E.3
  • 82
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants
    • Cock PJ, Fields CJ, Goto N, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants. Nucleic Acids Res 2010;38(6):1767-1771.
    • (2010) Nucleic Acids Res , vol.38 , Issue.6 , pp. 1767-1771
    • Cock, P.J.1    Fields, C.J.2    Goto, N.3
  • 83
    • 80755171163 scopus 로고    scopus 로고
    • Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
    • Hamada M, Wijaya E, Frith MC, et al. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics 2011;27(22):3085-3092.
    • (2011) Bioinformatics , vol.27 , Issue.22 , pp. 3085-3092
    • Hamada, M.1    Wijaya, E.2    Frith, M.C.3
  • 84
    • 77956873295 scopus 로고    scopus 로고
    • Disease-associated mutations that alter the RNA structural ensemble
    • Halvorsen M, Martin JS, Broadaway S, et al. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet 2010;6(8):e1001074.
    • (2010) PLoS Genet , vol.6 , Issue.8 , pp. e1001074
    • Halvorsen, M.1    Martin, J.S.2    Broadaway, S.3
  • 86
    • 0031721576 scopus 로고    scopus 로고
    • Dynamic programming alignment accuracy
    • Holmes I, Durbin R. Dynamic programming alignment accuracy. JComput Biol 1998;5(3):493-504.
    • (1998) JComput Biol , vol.5 , Issue.3 , pp. 493-504
    • Holmes, I.1    Durbin, R.2
  • 87
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • Knudsen B, Hein J. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999;15(6):446-454.
    • (1999) Bioinformatics , vol.15 , Issue.6 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 88
    • 33947417295 scopus 로고    scopus 로고
    • A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
    • Fariselli P, Martelli PL, Casadio R. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics 2005; 6(Suppl 4):S12.
    • (2005) BMC Bioinformatics , vol.6 , pp. S12
    • Fariselli, P.1    Martelli, P.L.2    Casadio, R.3
  • 89
    • 33845682909 scopus 로고    scopus 로고
    • Multiple alignment of protein sequences with repeats and rearrangements
    • Phuong TM, Do CB, Edgar RC, et al. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res 2006;34(20):5932-5942.
    • (2006) Nucleic Acids Res , vol.34 , Issue.20 , pp. 5932-5942
    • Phuong, T.M.1    Do, C.B.2    Edgar, R.C.3
  • 90
    • 77955352019 scopus 로고    scopus 로고
    • MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
    • Liu Y, Schmidt B, Maskell DL. MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics 2010;26(16):1958-1964.
    • (2010) Bioinformatics , vol.26 , Issue.16 , pp. 1958-1964
    • Liu, Y.1    Schmidt, B.2    Maskell, D.L.3
  • 91
    • 44349140636 scopus 로고    scopus 로고
    • R-Coffee: a method for multiple alignment of non-coding RNA
    • Wilm A, Higgins DG, Notredame C. R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res 2008;36:e52.
    • (2008) Nucleic Acids Res , vol.36 , pp. e52
    • Wilm, A.1    Higgins, D.G.2    Notredame, C.3
  • 92
    • 25444443637 scopus 로고    scopus 로고
    • Bayesian coestimation of phylogeny and sequence alignment
    • Lunter G, Miklos I, Drummond A, et al. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 2005;6:83.
    • (2005) BMC Bioinformatics , vol.6 , pp. 83
    • Lunter, G.1    Miklos, I.2    Drummond, A.3
  • 93
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inf 2009;23(1):205-211.
    • (2009) Genome Inf , vol.23 , Issue.1 , pp. 205-211
    • Eddy, S.R.1
  • 94
    • 44949157290 scopus 로고    scopus 로고
    • A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    • Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 2008;4(5):e1000069.
    • (2008) PLoS Comput Biol , vol.4 , Issue.5 , pp. e1000069
    • Eddy, S.R.1
  • 95
    • 9244264948 scopus 로고    scopus 로고
    • Parametric inference for biological sequence analysis
    • Pachter L, Sturmfels B. Parametric inference for biological sequence analysis. Proc Natl Acad Sci USA 2004;101(46):16138-16143.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.46 , pp. 16138-16143
    • Pachter, L.1    Sturmfels, B.2
  • 96
    • 33745584089 scopus 로고    scopus 로고
    • Parametric alignment of Drosophila genomes
    • Dewey CN, Huggins PM, Woods K, et al. Parametric alignment of Drosophila genomes. PLoS Comput Biol 2006;2(6):e73.
    • (2006) PLoS Comput Biol , vol.2 , Issue.6 , pp. e73
    • Dewey, C.N.1    Huggins, P.M.2    Woods, K.3
  • 98
    • 9244251033 scopus 로고    scopus 로고
    • Tropical geometry of statistical models
    • Pachter L, Sturmfels B. Tropical geometry of statistical models. ProcNatlAcad SciUSA 2004;101(46):16132-16137.
    • (2004) ProcNatlAcad SciUSA , vol.101 , Issue.46 , pp. 16132-16137
    • Pachter, L.1    Sturmfels, B.2
  • 99
    • 78649653300 scopus 로고    scopus 로고
    • Computational approaches for RNA energy parameter estimation
    • Andronescu M, Condon A, Hoos HH, et al. Computational approaches for RNA energy parameter estimation. RNA 2010;16(12):2304-2318.
    • (2010) RNA , vol.16 , Issue.12 , pp. 2304-2318
    • Andronescu, M.1    Condon, A.2    Hoos, H.H.3
  • 100
    • 77955572164 scopus 로고    scopus 로고
    • A non-parametric bayesian approach for predicting rna secondary structures
    • Sato K, Hamada M, Mituyama T, et al. A non-parametric bayesian approach for predicting rna secondary structures. J Bioinfor Comput Biol 2010;8(4):727-742.
    • (2010) J Bioinfor Comput Biol , vol.8 , Issue.4 , pp. 727-742
    • Sato, K.1    Hamada, M.2    Mituyama, T.3
  • 101
    • 84856001353 scopus 로고    scopus 로고
    • A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more
    • Rivas E, Lang R, Eddy SR. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more. RNA 2012;18(2):193-212.
    • (2012) RNA , vol.18 , Issue.2 , pp. 193-212
    • Rivas, E.1    Lang, R.2    Eddy, S.R.3
  • 103
    • 0037311782 scopus 로고    scopus 로고
    • Gene finding with a hidden Markov model of genome structure and evolution
    • Pedersen JS, Hein J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 2003;19:219-227.
    • (2003) Bioinformatics , vol.19 , pp. 219-227
    • Pedersen, J.S.1    Hein, J.2


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