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Volumn 9, Issue 1, 2014, Pages

Assessing the efficiency of multiple sequence alignment programs

Author keywords

Accuracy; Computer programs; Multiple sequence alignment; Performance

Indexed keywords


EID: 84899491312     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-9-4     Document Type: Article
Times cited : (79)

References (27)
  • 1
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 10.1016/0022-2836(70)90057-4, 5420325
    • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443-453. 10.1016/0022-2836(70)90057-4, 5420325.
    • (1970) J Mol Biol , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 2
    • 0019764298 scopus 로고
    • Comparative biosequence metrics
    • 10.1007/BF01733210, 7334527
    • Smith TF, Waterman MS, Fitch WM. Comparative biosequence metrics. J Mol Evol 1981, 18(1):38-46. 10.1007/BF01733210, 7334527.
    • (1981) J Mol Evol , vol.18 , Issue.1 , pp. 38-46
    • Smith, T.F.1    Waterman, M.S.2    Fitch, W.M.3
  • 3
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • 10.1007/BF02603120, 3118049
    • Feng DF, Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 1987, 25(4):351-360. 10.1007/BF02603120, 3118049.
    • (1987) J Mol Evol , vol.25 , Issue.4 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 4
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 10.1093/nar/22.22.4673, 308517, 7984417
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 5
    • 45949105543 scopus 로고    scopus 로고
    • DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
    • 10.1186/1748-7188-3-6, 2430965, 18505568
    • Subramanian AR, Kaufmann M, Morgenstern B. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol 2008, 3:6. 10.1186/1748-7188-3-6, 2430965, 18505568.
    • (2008) Algorithms Mol Biol , vol.3 , pp. 6
    • Subramanian, A.R.1    Kaufmann, M.2    Morgenstern, B.3
  • 6
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: a novel method for fast and accurate multiple sequence alignment
    • 10.1006/jmbi.2000.4042, 10964570
    • Notredame C, Higgins DG, Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205-217. 10.1006/jmbi.2000.4042, 10964570.
    • (2000) J Mol Biol , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 7
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: probabilistic consistency-based multiple sequence alignment
    • 10.1101/gr.2821705, 546535, 15687296
    • Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15(2):330-340. 10.1101/gr.2821705, 546535, 15687296.
    • (2005) Genome Res , vol.15 , Issue.2 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 8
    • 33751004142 scopus 로고    scopus 로고
    • Probalign: multiple sequence alignment using partition function posterior probabilities
    • 10.1093/bioinformatics/btl472, 16954142
    • Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006, 22(22):2715-2721. 10.1093/bioinformatics/btl472, 16954142.
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2715-2721
    • Roshan, U.1    Livesay, D.R.2
  • 10
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • 10.1093/bioinformatics/18.3.452, 11934745
    • Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452-464. 10.1093/bioinformatics/18.3.452, 11934745.
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 11
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • 10.1006/jmbi.1996.0679, 8980688
    • Gotoh O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 1996, 264(4):823-838. 10.1006/jmbi.1996.0679, 8980688.
    • (1996) J Mol Biol , vol.264 , Issue.4 , pp. 823-838
    • Gotoh, O.1
  • 12
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 2004, 5:113.
    • (2004) BMC Bioinforma , vol.5 , pp. 113
    • Edgar, R.C.1
  • 13
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • 10.1093/nar/gkf436, 135756, 12136088
    • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059-3066. 10.1093/nar/gkf436, 135756, 12136088.
    • (2002) Nucleic Acids Res , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 14
    • 0028928174 scopus 로고
    • Comprehensive study on iterative algorithms of multiple sequence alignment
    • Hirosawa M, Totoki Y, Hoshida M, Ishikawa M. Comprehensive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 1995, 11(1):13-18.
    • (1995) Comput Appl Biosci , vol.11 , Issue.1 , pp. 13-18
    • Hirosawa, M.1    Totoki, Y.2    Hoshida, M.3    Ishikawa, M.4
  • 15
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • 10.1093/nar/gki198, 548345, 15661851
    • Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33(2):511-518. 10.1093/nar/gki198, 548345, 15661851.
    • (2005) Nucleic Acids Res , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 16
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
    • 10.1002/prot.20527, 16044462
    • Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61(1):127-136. 10.1002/prot.20527, 16044462.
    • (2005) Proteins , vol.61 , Issue.1 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3    Poch, O.4
  • 17
    • 0035175770 scopus 로고    scopus 로고
    • BAliBASE (benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
    • 10.1093/nar/29.1.323, 29792, 11125126
    • Bahr A, Thompson JD, Thierry JC, Poch O. BAliBASE (benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res 2001, 29(1):323-326. 10.1093/nar/29.1.323, 29792, 11125126.
    • (2001) Nucleic Acids Res , vol.29 , Issue.1 , pp. 323-326
    • Bahr, A.1    Thompson, J.D.2    Thierry, J.C.3    Poch, O.4
  • 18
    • 43249091570 scopus 로고    scopus 로고
    • A new protein linear motif benchmark for multiple sequence alignment software
    • Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD. A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinforma 2008, 9:213.
    • (2008) BMC Bioinforma , vol.9 , pp. 213
    • Perrodou, E.1    Chica, C.2    Poch, O.3    Gibson, T.J.4    Thompson, J.D.5
  • 19
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • 10.1016/S0014-5793(02)03189-7, 12354624
    • Lassmann T, Sonnhammer EL. Quality assessment of multiple alignment programs. FEBS Lett 2002, 529(1):126-130. 10.1016/S0014-5793(02)03189-7, 12354624.
    • (2002) FEBS Lett , vol.529 , Issue.1 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 20
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • 10.1093/nar/27.13.2682, 148477, 10373585
    • Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 1999, 27(13):2682-2690. 10.1093/nar/27.13.2682, 148477, 10373585.
    • (1999) Nucleic Acids Res , vol.27 , Issue.13 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 21
    • 33748940447 scopus 로고    scopus 로고
    • Analysis and comparison of benchmarks for multiple sequence alignment
    • Blackshields G, Wallace IM, Larkin M, Higgins DG. Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol 2006, 6(4):321-339.
    • (2006) In Silico Biol , vol.6 , Issue.4 , pp. 321-339
    • Blackshields, G.1    Wallace, I.M.2    Larkin, M.3    Higgins, D.G.4
  • 22
    • 33750736013 scopus 로고    scopus 로고
    • The accuracy of several multiple sequence alignment programs for proteins
    • Nuin PA, Wang Z, Tillier ER. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinforma 2006, 7:471.
    • (2006) BMC Bioinforma , vol.7 , pp. 471
    • Nuin, P.A.1    Wang, Z.2    Tillier, E.R.3
  • 23
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers EW, Miller W. Optimal alignments in linear space. Comput Appl Biosci 1988, 4(1):11-17.
    • (1988) Comput Appl Biosci , vol.4 , Issue.1 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 24
    • 72549111108 scopus 로고    scopus 로고
    • Optimizing substitution matrix choice and gap parameters for sequence alignment
    • Edgar RC. Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinforma 2009, 10:396.
    • (2009) BMC Bioinforma , vol.10 , pp. 396
    • Edgar, R.C.1
  • 25
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • 10.1093/bib/bbn013, 18372315
    • Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9(4):286-298. 10.1093/bib/bbn013, 18372315.
    • (2008) Brief Bioinform , vol.9 , Issue.4 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 26
    • 77955019084 scopus 로고    scopus 로고
    • Parallelization of the MAFFT multiple sequence alignment program
    • 10.1093/bioinformatics/btq224, 2905546, 20427515
    • Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 2010, 26(15):1899-1900. 10.1093/bioinformatics/btq224, 2905546, 20427515.
    • (2010) Bioinformatics , vol.26 , Issue.15 , pp. 1899-1900
    • Katoh, K.1    Toh, H.2
  • 27
    • 77952039847 scopus 로고    scopus 로고
    • Sequence embedding for fast construction of guide trees for multiple sequence alignment
    • 10.1186/1748-7188-5-21, 2893182, 20470396
    • Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 2010, 5:21. 10.1186/1748-7188-5-21, 2893182, 20470396.
    • (2010) Algorithms Mol Biol , vol.5 , pp. 21
    • Blackshields, G.1    Sievers, F.2    Shi, W.3    Wilm, A.4    Higgins, D.G.5


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