메뉴 건너뛰기




Volumn 19, Issue 5, 2012, Pages 532-549

A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA)

Author keywords

algorithms; alignment; RNA; secondary structure; sequence analysis

Indexed keywords

ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; HUMAN; METHODOLOGY; REVIEW; STATISTICAL MODEL;

EID: 84860704698     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0197     Document Type: Review
Times cited : (14)

References (88)
  • 1
    • 77952882024 scopus 로고    scopus 로고
    • Prediction and design of DNA and RNA structures
    • Andersen, E.S. 2010. Prediction and design of DNA and RNA structures. N. Biotechnol. 27, 184-193.
    • (2010) N. Biotechnol. , vol.27 , pp. 184-193
    • Andersen, E.S.1
  • 2
    • 34547840261 scopus 로고    scopus 로고
    • Efficient parameter estimation for RNA secondary structure prediction
    • Andronescu, M., Condon, A., Hoos, H., et al. 2007. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 23, 19-28.
    • (2007) Bioinformatics , vol.23 , pp. 19-28
    • Andronescu, M.1    Condon, A.2    Hoos, H.3
  • 3
    • 78649653300 scopus 로고    scopus 로고
    • Computational approaches for RNA energy parameter estimation
    • Andronescu, M., Condon, A., Hoos, H.H., et al. 2010. Computational approaches for RNA energy parameter estimation. RNA 16, 2304-2318.
    • (2010) RNA , vol.16 , pp. 2304-2318
    • Andronescu, M.1    Condon, A.2    Hoos, H.H.3
  • 4
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi, P., Brunak, S., Chauvin, Y., et al. 2000. Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics 16, 412-424. (Pubitemid 30487963)
    • (2000) Bioinformatics , vol.16 , Issue.5 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.F.4    Nielsen, H.5
  • 5
    • 77957322715 scopus 로고    scopus 로고
    • ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
    • Bellaousov, S., and Mathews, D.H. 2010. ProbKnot: Fast prediction of RNA secondary structure including pseudoknots. RNA 16, 1870-1880.
    • (2010) RNA , vol.16 , pp. 1870-1880
    • Bellaousov, S.1    Mathews, D.H.2
  • 6
    • 58249121729 scopus 로고    scopus 로고
    • RNAalifold: Improved consensus structure prediction for RNA alignments
    • Bernhart, S., Hofacker, I., Will, S., et al. 2008. RNAalifold: Improved consensus structure prediction for RNA alignments. BMC Bioinform. 9, 474.
    • (2008) BMC Bioinform. , vol.9 , pp. 474
    • Bernhart, S.1    Hofacker, I.2    Will, S.3
  • 7
    • 34147112685 scopus 로고    scopus 로고
    • Noncoding RNA transcription beyond annotated genes
    • DOI 10.1016/j.gde.2007.02.008, PII S0959437X07000342, Chromosomes and Expression Mechanisms
    • Carninci, P., and Hayashizaki, Y. 2007. Noncoding RNA transcription beyond annotated genes. Curr. Opin. Genet. Dev. 17, 139-144. (Pubitemid 46553830)
    • (2007) Current Opinion in Genetics and Development , vol.17 , Issue.2 , pp. 139-144
    • Carninci, P.1    Hayashizaki, Y.2
  • 9
    • 77950538424 scopus 로고    scopus 로고
    • Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    • Dessimoz, C., and Gil, M. 2010. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol. 11, R37.
    • (2010) Genome Biol. , vol.11
    • Dessimoz, C.1    Gil, M.2
  • 10
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding, Y., Chan, C.Y., and Lawrence, C.E. 2004. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32, 135-141.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 135-141
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 11
    • 23644448438 scopus 로고    scopus 로고
    • RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
    • DOI 10.1261/rna.2500605
    • Ding, Y., Chan, C., and Lawrence, C. 2005. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166. (Pubitemid 41132387)
    • (2005) RNA , vol.11 , Issue.8 , pp. 1157-1166
    • Ding, Y.1    Chi, Y.C.2    Lawrence, C.E.3
  • 12
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • DOI 10.1101/gr.2821705
    • Do, C., Mahabhashyam, M., Brudno, M., et al. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 15, 330-340. (Pubitemid 40309398)
    • (2005) Genome Research , vol.15 , Issue.2 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 13
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • DOI 10.1093/bioinformatics/btl246
    • Do, C., Woods, D., and Batzoglou, S. 2006a. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22, e90-e98. (Pubitemid 44288277)
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 15
    • 46249114849 scopus 로고    scopus 로고
    • A max-margin model for efficient simultaneous alignment and folding of RNA sequences
    • DOI 10.1093/bioinformatics/btn177
    • Do, C., Foo, C., and Batzoglou, S. 2008. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics 24, i68-i76. (Pubitemid 351911659)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Do, C.B.1    Foo, C.-S.2    Batzoglou, S.3
  • 16
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    • Dowell, R., and Eddy, S. 2004. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. 5, 71.
    • (2004) BMC Bioinform. , vol.5 , pp. 71
    • Dowell, R.1    Eddy, S.2
  • 18
    • 3042739661 scopus 로고    scopus 로고
    • What is dynamic programming?
    • DOI 10.1038/nbt0704-909
    • Eddy, S.R. 2004. What is dynamic programming? Nat. Biotechnol. 22, 909-910. (Pubitemid 38886615)
    • (2004) Nature Biotechnology , vol.22 , Issue.7 , pp. 909-910
    • Eddy, S.R.1
  • 19
    • 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, P., and Casadio, R. 2005. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinform. 6, Suppl 4, S12.
    • (2005) BMC Bioinform. , vol.6 , Issue.SUPPL. 4
    • Fariselli, P.1    Martelli, P.2    Casadio, R.3
  • 20
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 21
    • 77649140807 scopus 로고    scopus 로고
    • Parameters for accurate genome alignment
    • Frith, M.C., Hamada, M., and Horton, P. 2010. Parameters for accurate genome alignment. BMC Bioinform. 11, 80.
    • (2010) BMC Bioinform. , vol.11 , pp. 80
    • Frith, M.C.1    Hamada, M.2    Horton, P.3
  • 22
    • 0036678616 scopus 로고    scopus 로고
    • Probabilistic alignment of motifs with sequences
    • Gonnet, P., and Lisacek, F. 2002. Probabilistic alignment of motifs with sequences. Bioinformatics 18, 1091-1101. (Pubitemid 34919230)
    • (2002) Bioinformatics , vol.18 , Issue.8 , pp. 1091-1101
    • Gonnet, P.1    Lisacek, F.2
  • 23
    • 40449115745 scopus 로고    scopus 로고
    • CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    • Gross, S., Do, C., Sirota, M., et al. 2007a. CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 8, R269.
    • (2007) Genome Biol. , vol.8
    • Gross, S.1    Do, C.2    Sirota, M.3
  • 24
    • 34548413443 scopus 로고    scopus 로고
    • Training conditional random fields for maximum labelwise accuracy, 529-536
    • In Schölkopf, B., Platt, J., and Hoffman, T., eds. MIT Press, Cambridge, MA
    • Gross, S.S., Russakovsky, O., Do, C.B., et al. 2007b. Training conditional random fields for maximum labelwise accuracy, 529-536. In Schölkopf, B., Platt, J., and Hoffman, T., eds. Advances in Neural Information Processing Systems 19. MIT Press, Cambridge, MA.
    • (2007) Advances in Neural Information Processing Systems 19
    • Gross, S.S.1    Russakovsky, O.2    Do, C.B.3
  • 25
    • 60149094002 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure using generalized centroid estimators
    • Hamada, M., Kiryu, H., Sato, K., et al. 2009a. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25, 465-473.
    • (2009) Bioinformatics , vol.25 , pp. 465-473
    • Hamada, M.1    Kiryu, H.2    Sato, K.3
  • 26
    • 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. 2009b. CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 25, 3236-3243.
    • (2009) Bioinformatics , vol.25 , pp. 3236-3243
    • Hamada, M.1    Sato, K.2    Kiryu, H.3
  • 27
    • 66349124254 scopus 로고    scopus 로고
    • Predictions of RNA secondary structure by combining homologous sequence information
    • Hamada, M., Sato, K., Kiryu, H., et al. 2009c. Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 25, i330-i338.
    • (2009) Bioinformatics , vol.25
    • Hamada, M.1    Sato, K.2    Kiryu, H.3
  • 28
    • 78649469968 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
    • Hamada, M., Sato, K., and Asai, K. 2010. Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. 11, 586.
    • (2010) BMC Bioinform. , vol.11 , pp. 586
    • Hamada, M.1    Sato, K.2    Asai, K.3
  • 29
    • 79951974555 scopus 로고    scopus 로고
    • Generalized centroid estimators in bioinformatics
    • Hamada, M., Kiryu, H., Iwasaki, W., et al. 2011a. Generalized centroid estimators in bioinformatics. PLoS ONE 6, e16450.
    • (2011) PLoS ONE , vol.6
    • Hamada, M.1    Kiryu, H.2    Iwasaki, W.3
  • 30
    • 79551480068 scopus 로고    scopus 로고
    • Improving the accuracy of predicting secondary structure for aligned RNA sequences
    • Hamada, M., Sato, K., and Asai, K. 2011b. Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. 39, 393-402.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 393-402
    • Hamada, M.1    Sato, K.2    Asai, K.3
  • 31
    • 79960025412 scopus 로고    scopus 로고
    • CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences
    • Hamada, M., Yamada, K., Sato, K., et al. 2011c. CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. 39, W100-W106.
    • (2011) Nucleic Acids Res. , vol.39
    • Hamada, M.1    Yamada, K.2    Sato, K.3
  • 32
    • 42449109109 scopus 로고    scopus 로고
    • PARTS: Probabilistic alignment for RNA joinT secondary structure prediction
    • DOI 10.1093/nar/gkn043
    • Harmanci, A., Sharma, G., and Mathews, D. 2008. PARTS: Probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Res. 36, 2406-2417. (Pubitemid 351567012)
    • (2008) Nucleic Acids Research , vol.36 , Issue.7 , pp. 2406-2417
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 33
    • 67651163664 scopus 로고    scopus 로고
    • Stochastic sampling of the RNA structural alignment space
    • Harmanci, A.O., Sharma, G., and Mathews, D.H. 2009. Stochastic sampling of the RNA structural alignment space. Nucleic Acids Res. 37, 4063-4075.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 4063-4075
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 34
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • DOI 10.1016/S0022-2836(02)00308-X
    • Hofacker, I.L., Fekete, M., and Stadler, P.F. 2002. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059-1066. (Pubitemid 34729418)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.5 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 35
    • 0031721576 scopus 로고    scopus 로고
    • Dynamic programming alignment accuracy
    • Holmes, I., and Durbin, R. 1998. Dynamic programming alignment accuracy. J. Comput. Biol. 5, 493-504. (Pubitemid 28436296)
    • (1998) Journal of Computational Biology , vol.5 , Issue.3 , pp. 493-504
    • Holmes, I.1    Durbin, R.2
  • 36
    • 66549104913 scopus 로고    scopus 로고
    • A maximum expected utility framework for binary sequence labeling
    • Jansche, M. 2007. A maximum expected utility framework for binary sequence labeling. Proc. ACL 736-743.
    • (2007) Proc. ACL , pp. 736-743
    • Jansche, M.1
  • 37
    • 29144483361 scopus 로고    scopus 로고
    • An HMM posterior decoder for sequence feature prediction that includes homology information
    • DOI 10.1093/bioinformatics/bti1014
    • Kall, L., Krogh, A., and Sonnhammer, E.L. 2005. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21, Suppl 1, i251-i257. (Pubitemid 41794496)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 38
    • 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. 2010. RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 26, i460-i466.
    • (2010) Bioinformatics , vol.26
    • Kato, Y.1    Sato, K.2    Hamada, M.3
  • 39
    • 44149125756 scopus 로고    scopus 로고
    • Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
    • Katoh, K., and Toh, H. 2008. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinform. 9, 212.
    • (2008) BMC Bioinform. , vol.9 , pp. 212
    • Katoh, K.1    Toh, H.2
  • 40
    • 33847262911 scopus 로고    scopus 로고
    • Robust prediction of consensus secondary structures using averaged base pairing probability matrices
    • DOI 10.1093/bioinformatics/btl636
    • Kiryu, H., Kin, T., and Asai, K. 2007a. Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics 23, 434-441. (Pubitemid 46323124)
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 434-441
    • Kiryu, H.1    Kin, T.2    Asai, K.3
  • 41
    • 34547844102 scopus 로고    scopus 로고
    • Murlet: A practical multiple alignment tool for structural RNA sequences
    • DOI 10.1093/bioinformatics/btm146
    • Kiryu, H., Tabei, Y., Kin, T., et al. 2007b. Murlet: A practical multiple alignment tool for structural RNA sequences. Bioinformatics 23, 1588-1598. (Pubitemid 47244448)
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 1588-1598
    • Kiryu, H.1    Tabei, Y.2    Kin, T.3    Asai, K.4
  • 42
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • DOI 10.1093/bioinformatics/15.6.446
    • Knudsen, B., and Hein, J. 1999. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15, 446-454. (Pubitemid 29361038)
    • (1999) Bioinformatics , vol.15 , Issue.6 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 43
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • DOI 10.1093/nar/gkg614
    • Knudsen, B., and Hein, J. 2003. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 31, 3423-3428. (Pubitemid 37442171)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 44
    • 33846204781 scopus 로고    scopus 로고
    • Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information
    • DOI 10.1002/prot.21240
    • Koike, R., Kinoshita, K., and Kidera, A. 2007. Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information. Proteins 66, 655-663. (Pubitemid 46106769)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.3 , pp. 655-663
    • Koike, R.1    Kinoshita, K.2    Kidera, A.3
  • 45
    • 77955352019 scopus 로고    scopus 로고
    • MSAProbs: Multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
    • Liu, Y., Schmidt, B., and Maskell, D.L. 2010. MSAProbs: Multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics 26, 1958-1964.
    • (2010) Bioinformatics , vol.26 , pp. 1958-1964
    • Liu, Y.1    Schmidt, B.2    Maskell, D.L.3
  • 46
    • 79551535532 scopus 로고    scopus 로고
    • Computing the partition function for kinetically trapped RNA secondary structures
    • Lorenz, W.A., and Clote, P. 2011. Computing the partition function for kinetically trapped RNA secondary structures. PLoS ONE 6, e16178.
    • (2011) PLoS ONE , vol.6
    • Lorenz, W.A.1    Clote, P.2
  • 47
    • 70349131635 scopus 로고    scopus 로고
    • Improved RNA secondary structure prediction by maximizing expected pair accuracy
    • Lu, Z.J., Gloor, J.W., and Mathews, D.H. 2009. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 15, 1805-1813.
    • (2009) RNA , vol.15 , pp. 1805-1813
    • Lu, Z.J.1    Gloor, J.W.2    Mathews, D.H.3
  • 48
    • 25444443637 scopus 로고    scopus 로고
    • Bayesian coestimation of phylogeny and sequence alignment
    • Lunter, G., Miklos, I., Drummond, A., et al. 2005. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinform. 6, 83.
    • (2005) BMC Bioinform. , vol.6 , pp. 83
    • Lunter, G.1    Miklos, I.2    Drummond, A.3
  • 49
    • 39049145326 scopus 로고    scopus 로고
    • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    • DOI 10.1101/gr.6725608
    • Lunter, G., Rocco, A., Mimouni, N., et al. 2008. Uncertainty in homology inferences: Assessing and improving genomic sequence alignment. Genome Res. 18, 298-309. (Pubitemid 351240740)
    • (2008) Genome Research , vol.18 , Issue.2 , pp. 298-309
    • Lunter, G.1    Rocco, A.2    Mimouni, N.3    Heger, A.4    Caldeira, A.5    Hein, J.6
  • 50
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • DOI 10.1006/jmbi.1999.2700
    • Mathews, D.H., Sabina, J., Zuker, M., et al. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940. (Pubitemid 29248642)
    • (1999) Journal of Molecular Biology , vol.288 , Issue.5 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 52
    • 24644443227 scopus 로고    scopus 로고
    • The functional genomics of noncoding RNA
    • DOI 10.1126/science.1117806
    • Mattick, J. 2005. The functional genomics of noncoding RNA. Science 309, 1527-1528. (Pubitemid 41266470)
    • (2005) Science , vol.309 , Issue.5740 , pp. 1527-1528
    • Mattick, J.S.1
  • 53
    • 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. (Pubitemid 20145703)
    • (1990) Biopolymers , vol.29 , Issue.6-7 , pp. 1105-1119
    • McCaskill, J.S.1
  • 54
    • 5744249209 scopus 로고
    • Equations of state calculations by fast computing machine
    • Metropolis, N., Rosenbluth, A., Teller, M., et al. 1953. Equations of state calculations by fast computing machine. J. Chem. Phys. 21, 1087-1091.
    • (1953) J. Chem. Phys. , vol.21 , pp. 1087-1091
    • Metropolis, N.1    Rosenbluth, A.2    Teller, M.3
  • 55
    • 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. (Pubitemid 26008492)
    • (1995) Protein Engineering , vol.8 , Issue.10 , pp. 999-1009
    • Miyazawa, S.1
  • 56
    • 84871614279 scopus 로고    scopus 로고
    • The highest expected reward decoding for hmms with application to recombination detection
    • Nánási, M., Vinar, T., and Brejová, B. 2010. The highest expected reward decoding for hmms with application to recombination detection. Proc. CPM '10 164-176.
    • (2010) Proc. CPM , vol.10 , pp. 164-176
    • Nánási, M.1    Vinar, T.2    Brejová, B.3
  • 58
    • 58149236993 scopus 로고    scopus 로고
    • Exact calculation of distributions on integers, with application to sequence alignment
    • Newberg, L.A., and Lawrence, C.E. 2009. Exact calculation of distributions on integers, with application to sequence alignment. J. Comput. Biol. 16, 1-18.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1-18
    • Newberg, L.A.1    Lawrence, C.E.2
  • 60
    • 44949202369 scopus 로고    scopus 로고
    • Multiple protein sequence alignment
    • Pei, J. 2008. Multiple protein sequence alignment. Curr. Opin. Struct. Biol. 18, 382-386.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 382-386
    • Pei, J.1
  • 61
    • 33845682909 scopus 로고    scopus 로고
    • Multiple alignment of protein sequences with repeats and rearrangements
    • DOI 10.1093/nar/gkl511
    • Phuong, T.M., Do, C.B., Edgar, R.C., et al. 2006. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res. 34, 5932-5942. (Pubitemid 44941172)
    • (2006) Nucleic Acids Research , vol.34 , Issue.20 , pp. 5932-5942
    • Phuong, T.M.1    Do, C.B.2    Edgar, R.C.3    Batzoglou, S.4
  • 62
    • 77952765712 scopus 로고    scopus 로고
    • Computational methods for ab initio and comparative gene finding
    • Picardi, E., and Pesole, G. 2010. Computational methods for ab initio and comparative gene finding. Methods Mol. Biol. 609, 269-284.
    • (2010) Methods Mol. Biol. , vol.609 , pp. 269-284
    • Picardi, E.1    Pesole, G.2
  • 63
    • 84934442467 scopus 로고    scopus 로고
    • Multiple sequence alignment
    • Pirovano, W., and Heringa, J. 2008. Multiple sequence alignment. Methods Mol. Biol. 452, 143-161.
    • (2008) Methods Mol. Biol. , vol.452 , pp. 143-161
    • Pirovano, W.1    Heringa, J.2
  • 64
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Robinson, D.F., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 65
    • 33751004142 scopus 로고    scopus 로고
    • Probalign: Multiple sequence alignment using partition function posterior probabilities
    • DOI 10.1093/bioinformatics/btl472
    • Roshan, U., and Livesay, D. 2006. Probalign: Multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22, 2715-2721. (Pubitemid 44742389)
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2715-2721
    • Roshan, U.1    Livesay, D.R.2
  • 66
    • 77956098140 scopus 로고    scopus 로고
    • PicXAA: Greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
    • Sahraeian, S.M., and Yoon, B.J. 2010. PicXAA: Greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Res. 38, 4917-4928.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4917-4928
    • Sahraeian, S.M.1    Yoon, B.J.2
  • 67
    • 79951529676 scopus 로고    scopus 로고
    • PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
    • Sahraeian, S.M., and Yoon, B.J. 2011. PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinform. 12, Suppl 1, S38.
    • (2011) BMC Bioinform. , vol.12 , Issue.SUPPL. 1
    • Sahraeian, S.M.1    Yoon, B.J.2
  • 68
    • 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. (Pubitemid 15563502)
    • (1985) SIAM Journal on Applied Mathematics , vol.45 , Issue.5 , pp. 810-825
    • Sankoff David1
  • 69
    • 79959465715 scopus 로고    scopus 로고
    • IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
    • Sato, K., Kato, Y., Hamada, M., et al. 2011. IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 27, i85-i93.
    • (2011) Bioinformatics , vol.27
    • Sato, K.1    Kato, Y.2    Hamada, M.3
  • 70
    • 33746715541 scopus 로고    scopus 로고
    • A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    • Schultz, A.K., Zhang, M., Leitner, T., et al. 2006. A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinform. 7, 265.
    • (2006) BMC Bioinform. , vol.7 , pp. 265
    • Schultz, A.K.1    Zhang, M.2    Leitner, T.3
  • 72
    • 33846659941 scopus 로고    scopus 로고
    • Multiple alignment by sequence annealing
    • DOI 10.1093/bioinformatics/btl311
    • Schwartz, A., and Pachter, L. 2007. Multiple alignment by sequence annealing. Bioinformatics 23, e24-e29. (Pubitemid 46189631)
    • (2007) Bioinformatics , vol.23 , Issue.2
    • Schwartz, A.S.1    Pachter, L.2
  • 74
    • 56649099274 scopus 로고    scopus 로고
    • Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
    • Seemann, S., Gorodkin, J., and Backofen, R. 2008. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res. 36, 6355-6362.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6355-6362
    • Seemann, S.1    Gorodkin, J.2    Backofen, R.3
  • 75
    • 78651415661 scopus 로고    scopus 로고
    • PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences
    • Seemann, S.E., Richter, A.S., Gesell, T., et al. 2011. PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics 27, 211-219.
    • (2011) Bioinformatics , vol.27 , pp. 211-219
    • Seemann, S.E.1    Richter, A.S.2    Gesell, T.3
  • 76
    • 36949006682 scopus 로고    scopus 로고
    • MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules
    • Sinha, S., and He, X. 2007. MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PLoS Comput. Biol. 3, e216.
    • (2007) PLoS Comput. Biol. , vol.3
    • Sinha, S.1    He, X.2
  • 77
    • 38949138554 scopus 로고    scopus 로고
    • Computational prediction of protein-protein interactions
    • DOI 10.1007/s12033-007-0069-2
    • Skrabanek, L., Saini, H. K., Bader, G. D., et al. 2008. Computational prediction of protein-protein interactions. Mol. Biotechnol. 38, 1-17. (Pubitemid 351378094)
    • (2008) Molecular Biotechnology , vol.38 , Issue.1 , pp. 1-17
    • Skrabanek, L.1    Saini, H.K.2    Bader, G.D.3    Enright, A.J.4
  • 78
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T. F., and Waterman, M. S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 79
    • 32544440797 scopus 로고    scopus 로고
    • RNAshapes: An integrated RNA analysis package based on abstract shapes
    • DOI 10.1093/bioinformatics/btk010
    • Steffen, P., Voss, B., Rehmsmeier, M., et al. 2006. RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics 22, 500-503. (Pubitemid 43231429)
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 500-503
    • Steffen, P.1    Voss, B.2    Rehmsmeier, M.3    Reeder, J.4    Giegerich, R.5
  • 80
    • 84860500490 scopus 로고    scopus 로고
    • Training conditional random fields with multivariate evaluation measures
    • Suzuki, J., McDermott, E., and Isozaki, H. 2006. Training conditional random fields with multivariate evaluation measures. Proc. ACL 217-224.
    • (2006) Proc. ACL , pp. 217-224
    • Suzuki, J.1    McDermott, E.2    Isozaki, H.3
  • 81
    • 66349128376 scopus 로고    scopus 로고
    • A local multiple alignment method for detection of non-coding RNA sequences
    • Tabei, Y., and Asai, K. 2009. A local multiple alignment method for detection of non-coding RNA sequences. Bioinformatics 25, 1498-1505.
    • (2009) Bioinformatics , vol.25 , pp. 1498-1505
    • Tabei, Y.1    Asai, K.2
  • 82
    • 44949258055 scopus 로고    scopus 로고
    • Measuring global credibility with application to local sequence alignment
    • Webb-Robertson, B. J., McCue, L. A., and Lawrence, C. E. 2008. Measuring global credibility with application to local sequence alignment. PLoS Comput. Biol. 4, e1000077.
    • (2008) PLoS Comput. Biol. , vol.4
    • Webb-Robertson, B.J.1    McCue, L.A.2    Lawrence, C.E.3
  • 83
    • 80052736874 scopus 로고    scopus 로고
    • RNAG: A new GIBBS sampler for predicting RNA secondary structure for unaligned sequences
    • Wei, D., Alpert, L.V., and Lawrence, C.E. 2011. RNAG: A new GIBBS sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics 27, 2486-2493.
    • (2011) Bioinformatics , vol.27 , pp. 2486-2493
    • Wei, D.1    Alpert, L.V.2    Lawrence, C.E.3
  • 84
    • 84934434878 scopus 로고    scopus 로고
    • Inferring trees
    • Whelan, S. 2008. Inferring trees. Methods Mol. Biol. 452, 287-309.
    • (2008) Methods Mol. Biol. , vol.452 , pp. 287-309
    • Whelan, S.1
  • 85
    • 44349140636 scopus 로고    scopus 로고
    • R-Coffee: A method for multiple alignment of non-coding RNA
    • Wilm, A., Higgins, D., and Notredame, C. 2008. R-Coffee: A method for multiple alignment of non-coding RNA. Nucleic Acids Res. 36, e52.
    • (2008) Nucleic Acids Res. , vol.36
    • Wilm, A.1    Higgins, D.2    Notredame, C.3
  • 86
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • DOI 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G
    • Wuchty, S., Fontana, W., Hofacker, I. L., et al. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49, 145-165. (Pubitemid 29061655)
    • (1999) Biopolymers , vol.49 , Issue.2 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 87
    • 76249130835 scopus 로고    scopus 로고
    • Improvement in speed and accuracy of multiple sequence alignment program prime
    • Yamada, S., Osamu, G., and Hayato, Y. 2008. Improvement in speed and accuracy of multiple sequence alignment program prime. IPSJ Trans. Bioinform. (TBIO) 1, 2-12.
    • (2008) IPSJ Trans. Bioinform. (TBIO) , vol.1 , pp. 2-12
    • Yamada, S.1    Osamu, G.2    Hayato, Y.3
  • 88
    • 79957514991 scopus 로고    scopus 로고
    • Phylogeny inference based on spectral graph clustering
    • Zhang, S.B., Zhou, S.Y., He, J.G., et al. 2011. Phylogeny inference based on spectral graph clustering. J. Comput. Biol. 18, 627-637.
    • (2011) J. Comput. Biol. , vol.18 , pp. 627-637
    • Zhang, S.B.1    Zhou, S.Y.2    He, J.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.