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Volumn 41, Issue 1, 2013, Pages

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BALIBASE; BIOINFORMATICS; CONTROLLED STUDY; GENETIC DATABASE; MATHEMATICAL ANALYSIS; METHODOLOGY; MULTIPLE SEQUENCE ALIGNMENT; PREDICTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SUPPORT VECTOR MACHINE;

EID: 84871727826     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks919     Document Type: Article
Times cited : (11)

References (47)
  • 2
    • 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
  • 3
    • 79959981766 scopus 로고    scopus 로고
    • IPBA: A tool for protein structure comparison using sequence alignment strategies
    • Gelly, J.C., Joseph, A.P., Srinivasan, N. and de Brevern, A.G. (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res., 39, W18-W23.
    • (2011) Nucleic Acids Res. , vol.39
    • Gelly, J.C.1    Joseph, A.P.2    Srinivasan, N.3    De Brevern, A.G.4
  • 5
    • 79957621519 scopus 로고    scopus 로고
    • Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed
    • Hicks, S., Wheeler, D.A., Plon, S.E. and Kimmel, M. (2011) Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum. Mutat., 32, 661-668.
    • (2011) Hum. Mutat. , vol.32 , pp. 661-668
    • Hicks, S.1    Wheeler, D.A.2    Plon, S.E.3    Kimmel, M.4
  • 6
    • 79951537034 scopus 로고    scopus 로고
    • RNA-RNA interaction prediction based on multiple sequence alignments
    • Li, A.X., Marz, M., Qin, J. and Reidys, C.M. (2011) RNA-RNA interaction prediction based on multiple sequence alignments. Bioinformatics, 27, 456-463.
    • (2011) Bioinformatics , vol.27 , pp. 456-463
    • Li, A.X.1    Marz, M.2    Qin, J.3    Reidys, C.M.4
  • 7
    • 70349866695 scopus 로고    scopus 로고
    • Upcoming challenges for multiple sequence alignment methods in the high-throughput era
    • Kemena, C. and Notredame, C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
    • (2009) Bioinformatics , vol.25 , pp. 2455-2465
    • Kemena, C.1    Notredame, C.2
  • 8
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform., 11, 473-483.
    • (2010) Brief. Bioinform. , vol.11 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 9
    • 0027968068 scopus 로고
    • ClustalW: Improving the sensitivity of progressive multiple sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) ClustalW: improving the sensitivity of progressive multiple sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 10
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 11
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol Biol., 302, 205-217.
    • (2000) J. Mol Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 12
    • 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
  • 13
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: Combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G. and Notredame, C. (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340, 385-395.
    • (2004) J. Mol. Biol. , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 14
    • 34248532415 scopus 로고    scopus 로고
    • PROMALS: Towards accurate multiple sequence alignments of distantly related proteins
    • Pei, J. and Grishin, N.V. (2007) PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
    • (2007) Bioinformatics , vol.23 , pp. 802-808
    • Pei, J.1    Grishin, N.V.2
  • 18
    • 33750736013 scopus 로고    scopus 로고
    • The accuracy of several multiple sequence alignment programs for proteins
    • Nuin, P.A.S., Wang, Z.Z. and Elisabeth, R.M. (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics, 7, 471.
    • (2006) BMC Bioinformatics , vol.7 , pp. 471
    • Nuin, P.A.S.1    Wang, Z.Z.2    Elisabeth, R.M.3
  • 19
    • 77952297501 scopus 로고    scopus 로고
    • Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
    • Sierk, M.L., Smoot, M.E., Bass, E.J. and Pearson, W.R. (2010) Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. BMC Bioinformatics, 11, 146.
    • (2010) BMC Bioinformatics , vol.11 , pp. 146
    • Sierk, M.L.1    Smoot, M.E.2    Bass, E.J.3    Pearson, W.R.4
  • 20
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
    • Thompson, J.D., Koehl, P., Ripp, R. and Poch, O. (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3    Poch, O.4
  • 22
    • 0346494946 scopus 로고    scopus 로고
    • HOMSTRAD: Recent developments of the homologous protein structure alignment database
    • Stebbings, L.A. and Mizuguchi, K. (2004) HOMSTRAD: recent developments of the homologous protein structure alignment database. Nucleic Acids Res., 32, D203-D207.
    • (2004) Nucleic Acids Res. , vol.32
    • Stebbings, L.A.1    Mizuguchi, K.2
  • 23
    • 29244447181 scopus 로고    scopus 로고
    • Kalign-an accurate and fast multiple sequence alignment algorithm
    • Lassmann, T. and Sonnhammer, E.L. (2005) Kalign-an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics, 6, 298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 298
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 24
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 25
    • 78549270123 scopus 로고    scopus 로고
    • Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
    • Szabo, A., Novak, A., Miklos, I. and Hein, J. (2010) Reticular alignment: a progressive corner-cutting method for multiple sequence alignment. BMC Bioinformatics, 11, 570.
    • (2010) BMC Bioinformatics , vol.11 , pp. 570
    • Szabo, A.1    Novak, A.2    Miklos, I.3    Hein, J.4
  • 26
    • 84976654685 scopus 로고
    • Fast text searching allowing errors
    • Wu, S. and Manber, U. (1992) Fast text searching allowing errors. Commun. ACM, 35, 83-91.
    • (1992) Commun. ACM , vol.35 , pp. 83-91
    • Wu, S.1    Manber, U.2
  • 27
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B., Mahabhashyam, M.S.P., Brudno, M. and Batzoglou, S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res. , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 29
    • 78049380545 scopus 로고    scopus 로고
    • AlexSys: A knowledge-based expert system for multiple sequence alignment construction and analysis
    • Aniba, M.R., Poch, O., Marchler-Bauer, A. and Thompson, J.D. (2010) AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res., 38, 6338-6349.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6338-6349
    • Aniba, M.R.1    Poch, O.2    Marchler-Bauer, A.3    Thompson, J.D.4
  • 30
    • 33646358998 scopus 로고    scopus 로고
    • Prediction of yeast protein-protein interaction network: Insights from the Gene Ontology and annotations
    • Wu, X.M., Zhu, L., Guo, J., Zhang, D.Y. and Lin, K. (2006) Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res., 34, 2137-2150.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2137-2150
    • Wu, X.M.1    Zhu, L.2    Guo, J.3    Zhang, D.Y.4    Lin, K.5
  • 31
    • 77953360440 scopus 로고    scopus 로고
    • Utilizing shared interacting domain patterns and Gene Ontology information to improve protein-protein interaction prediction
    • Roslan, R., Othman, R.M., Shah, Z.A., Kasim, S., Asmuni, H., Taliba, J., Hassan, R. and Zakaria, Z. (2010) Utilizing shared interacting domain patterns and Gene Ontology information to improve protein-protein interaction prediction. Comput. Biol. Med., 40, 555-564.
    • (2010) Comput. Biol. Med. , vol.40 , pp. 555-564
    • Roslan, R.1    Othman, R.M.2    Shah, Z.A.3    Kasim, S.4    Asmuni, H.5    Taliba, J.6    Hassan, R.7    Zakaria, Z.8
  • 34
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy
    • Peng, H., Long, F. and Ding, C. (2005) Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell., 27, 1226-1238.
    • (2005) IEEE Trans. Pattern Anal. Mach. Intell. , vol.27 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 36
    • 65949090530 scopus 로고    scopus 로고
    • Sparse representation based on projection method in online least squares support vector machines
    • Li, L., Su, H. and Chu, J. (2009) Sparse representation based on projection method in online least squares support vector machines. J. Control Theory Appl., 7, 163-168.
    • (2009) J. Control Theory Appl. , vol.7 , pp. 163-168
    • Li, L.1    Su, H.2    Chu, J.3
  • 38
    • 79956190847 scopus 로고    scopus 로고
    • SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation
    • Anderson, C.L., Strope, C.L. and Moriyama, E.N. (2011) SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics, 12, 184.
    • (2011) BMC Bioinformatics , vol.12 , pp. 184
    • Anderson, C.L.1    Strope, C.L.2    Moriyama, E.N.3
  • 46
    • 0000135303 scopus 로고
    • Methods of conjugate gradients for solving linear systems
    • Hestenes, M.R. and Stiefel, E. (1952) Methods of conjugate gradients for solving linear systems. J. Res. Natl. Bur. Stand., 49, 409-436.
    • (1952) J. Res. Natl. Bur. Stand. , vol.49 , pp. 409-436
    • Hestenes, M.R.1    Stiefel, E.2
  • 47
    • 32944462016 scopus 로고    scopus 로고
    • Mutual information for the selection of relevant variables in spectrometric nonlinear modelling
    • Rossi, F., Lendasse, A., Francois, D., Wertz, V. and Verleysen, M. (2006) Mutual information for the selection of relevant variables in spectrometric nonlinear modelling. Chemometrics Intell. Lab. Syst., 80, 215-226.
    • (2006) Chemometrics Intell. Lab. Syst. , vol.80 , pp. 215-226
    • Rossi, F.1    Lendasse, A.2    Francois, D.3    Wertz, V.4    Verleysen, M.5


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