메뉴 건너뛰기




Volumn 441, Issue 1-2, 2009, Pages 141-147

Characterization of pairwise and multiple sequence alignment errors

Author keywords

Alignment errors; Multiple sequence alignment; Pairwise sequence alignment

Indexed keywords

ARTICLE; CONTROLLED STUDY; ERROR; GENE SEQUENCE; INTERMETHOD COMPARISON; MOLECULAR EVOLUTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SIMULATION;

EID: 67349247098     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.05.016     Document Type: Article
Times cited : (34)

References (41)
  • 1
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: probabilistic consistency-based multiple sequence alignment
    • Do C.B., Mahabhashyam M.S., Brudno M., and Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15 2 (2005) 330-340
    • (2005) Genome Res. , vol.15 , Issue.2 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 3
    • 0028828164 scopus 로고
    • Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences
    • Ellis J., and Morrison D. Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences. Parasitol. Res. 81 (1995) 696-699
    • (1995) Parasitol. Res. , vol.81 , pp. 696-699
    • Ellis, J.1    Morrison, D.2
  • 4
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng D.F., and Doolittle R.F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25 (1987) 351-360
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 5
    • 2342421929 scopus 로고    scopus 로고
    • On the significance of sequence alignments when using multiple scoring matrices
    • Frommlet F., Futschik A., and Bogdan M. On the significance of sequence alignments when using multiple scoring matrices. Bioinformatics 20 (2004) 881-887
    • (2004) Bioinformatics , vol.20 , pp. 881-887
    • Frommlet, F.1    Futschik, A.2    Bogdan, M.3
  • 6
    • 0026913444 scopus 로고
    • Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons
    • Goldstein L., and Waterman M.S. Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons. Bull. Math. Biol. 54 (1992) 785-812
    • (1992) Bull. Math. Biol. , vol.54 , pp. 785-812
    • Goldstein, L.1    Waterman, M.S.2
  • 7
    • 35848948397 scopus 로고    scopus 로고
    • Mind the gaps: evidence of bias in estimates of multiple sequence alignments
    • Golubchik T., Wise M.J., Easteal S., and Jermiin L.S. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol. Biol. Evol. 24 11 (2007) 2433-2442
    • (2007) Mol. Biol. Evol. , vol.24 , Issue.11 , pp. 2433-2442
    • Golubchik, T.1    Wise, M.J.2    Easteal, S.3    Jermiin, L.S.4
  • 8
    • 0025138774 scopus 로고
    • Consistency of optimal sequence alignments
    • Gotoh O. Consistency of optimal sequence alignments. Bull. Math. Biol. 52 (1990) 509-525
    • (1990) Bull. Math. Biol. , vol.52 , pp. 509-525
    • Gotoh, O.1
  • 10
    • 0026325708 scopus 로고
    • Playing with blocks: some pitfalls of forcing multiple alignments
    • Henikoff S. Playing with blocks: some pitfalls of forcing multiple alignments. New Biol. 3 (1991) 1148-1154
    • (1991) New Biol. , vol.3 , pp. 1148-1154
    • Henikoff, S.1
  • 11
    • 0034043777 scopus 로고    scopus 로고
    • The performance of several multiple sequence alignment programs in relation to secondary-structure features for an rRNA sequence
    • Hickson R.E., Simon C., and Perrey S.W. The performance of several multiple sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol. Biol. Evol. 17 (2000) 530-539
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 530-539
    • Hickson, R.E.1    Simon, C.2    Perrey, S.W.3
  • 12
    • 0028928174 scopus 로고
    • Comprehensive study on iterative algorithms of multiple sequence alignment
    • Hirosawa M., Totoki Y., Hoshida M., and Ishikawa M. Comprehensive study on iterative algorithms of multiple sequence alignment. Comput. Appl. Biosci. 11 (1995) 13-18
    • (1995) Comput. Appl. Biosci. , vol.11 , pp. 13-18
    • Hirosawa, M.1    Totoki, Y.2    Hoshida, M.3    Ishikawa, M.4
  • 13
    • 0031721576 scopus 로고    scopus 로고
    • Dynamic programming alignment accuracy
    • Holmes I., and Durbin R. Dynamic programming alignment accuracy. J. Comput. Biol. 5 (1998) 493-504
    • (1998) J. Comput. Biol. , vol.5 , pp. 493-504
    • Holmes, I.1    Durbin, R.2
  • 14
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K., Kuma K., Toh H., and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33 2 (2005) 511-518
    • (2005) Nucleic Acids Res. , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 15
    • 33846869288 scopus 로고    scopus 로고
    • Multiple sequence alignment: in pursuit of homologous DNA positions
    • Kumar S., and Filipski A. Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Res. 17 (2007) 127-135
    • (2007) Genome Res. , vol.17 , pp. 127-135
    • Kumar, S.1    Filipski, A.2
  • 16
    • 0025905252 scopus 로고
    • The order of sequence alignment can bias the selection of tree topology
    • Lake J.A. The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 8 (1991) 378-385
    • (1991) Mol. Biol. Evol. , vol.8 , pp. 378-385
    • Lake, J.A.1
  • 17
    • 34548088457 scopus 로고    scopus 로고
    • Heads or tails: a simple reliability check for multiple sequence alignments
    • Landan G., and Graur D. Heads or tails: a simple reliability check for multiple sequence alignments. Mol. Biol. Evol. 24 (2007) 1380-1383
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1380-1383
    • Landan, G.1    Graur, D.2
  • 18
    • 40549095323 scopus 로고    scopus 로고
    • Local reliability measures from sets of co-optimal multiple sequence alignments
    • Landan G., and Graur D. Local reliability measures from sets of co-optimal multiple sequence alignments. Pac. Symp. Biocomput. 13 (2008) 15-24
    • (2008) Pac. Symp. Biocomput. , vol.13 , pp. 15-24
    • Landan, G.1    Graur, D.2
  • 19
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann T., and Sonnhammer E.L. Quality assessment of multiple alignment programs. FEBS Lett. 529 (2002) 126-130
    • (2002) FEBS Lett. , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 20
    • 0028341506 scopus 로고
    • Comparative analysis of multiple protein-sequence alignment methods
    • McClure M.A., Vasi T.K., and Fitch W.M. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11 (1994) 571-592
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 571-592
    • McClure, M.A.1    Vasi, T.K.2    Fitch, W.M.3
  • 21
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa
    • Morrison D.A., and Ellis J.T. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa. Mol. Biol. Evol. 14 (1997) 428-441
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 22
    • 0038802447 scopus 로고    scopus 로고
    • Multiple sequence alignment - the gateway to further analysis
    • Mullan L.J. Multiple sequence alignment - the gateway to further analysis. Brief. Bioinform. 3 (2002) 303-305
    • (2002) Brief. Bioinform. , vol.3 , pp. 303-305
    • Mullan, L.J.1
  • 23
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 24
    • 0036189312 scopus 로고    scopus 로고
    • Nicholas, H.B., Ropelewski, A.J., Deerfield, D.W., 2002. Strategies for multiple sequence alignment. Biotechniques. 32:572-4., 576, 578.
    • Nicholas, H.B., Ropelewski, A.J., Deerfield, D.W., 2002. Strategies for multiple sequence alignment. Biotechniques. 32:572-4., 576, 578.
  • 25
    • 0036208872 scopus 로고    scopus 로고
    • Recent progress in multiple sequence alignment: a survey
    • Notredame C. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics 3 (2002) 131-144
    • (2002) Pharmacogenomics , vol.3 , pp. 131-144
    • Notredame, C.1
  • 26
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • Notredame C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol. 3 8 (2007) e123
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.8
    • Notredame, C.1
  • 27
    • 0032420579 scopus 로고    scopus 로고
    • Empirical estimation of the reliability of ribosomal RNA alignments
    • O'Brien E.A., and Higgins D.G. Empirical estimation of the reliability of ribosomal RNA alignments. Bioinformatics 14 (1998) 830-838
    • (1998) Bioinformatics , vol.14 , pp. 830-838
    • O'Brien, E.A.1    Higgins, D.G.2
  • 28
    • 33744993430 scopus 로고    scopus 로고
    • Multiple sequence alignment accuracy and phylogenetic inference
    • Ogden T.H., and Rosenberg M.S. Multiple sequence alignment accuracy and phylogenetic inference. Syst. Biol 55 (2006) 314-328
    • (2006) Syst. Biol , vol.55 , pp. 314-328
    • Ogden, T.H.1    Rosenberg, M.S.2
  • 29
  • 30
    • 0031857684 scopus 로고    scopus 로고
    • Rose: generating sequence families
    • Stoye J., Evers D., and Meyer F. Rose: generating sequence families. Bioinformatics 14 (1998) 157-163
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 31
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 32
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson J.D., Plewniak F., and Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27 (1999) 2682-2690
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 33
    • 0026458222 scopus 로고
    • Freeing phylogenies from artifacts of alignment
    • Thorne J.L., and Kishino H. Freeing phylogenies from artifacts of alignment. Mol. Biol. Evol. 9 (1992) 1148-1162
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 1148-1162
    • Thorne, J.L.1    Kishino, H.2
  • 34
    • 0026528734 scopus 로고
    • Inching toward reality: an improved likelihood model of sequence evolution
    • Thorne J.L., Kishino H., and Felsenstein J. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34 (1992) 3-16
    • (1992) J. Mol. Evol. , vol.34 , pp. 3-16
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 35
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: combining multiple sequence alignment methods with T-Coffee
    • Wallace I.M., O'Sullivan O., Higgins D.G., and Notredame C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34 6 (2006) 1692-1699
    • (2006) Nucleic Acids Res. , vol.34 , Issue.6 , pp. 1692-1699
    • Wallace, I.M.1    O'Sullivan, O.2    Higgins, D.G.3    Notredame, C.4
  • 36
    • 0028782102 scopus 로고
    • Estimating statistical significance of sequence alignments
    • Waterman M.S. Estimating statistical significance of sequence alignments. Philos. Trans. R. Soc. Lond., B Biol. Sci. 344 (1994) 383-390
    • (1994) Philos. Trans. R. Soc. Lond., B Biol. Sci. , vol.344 , pp. 383-390
    • Waterman, M.S.1
  • 38
    • 0028234758 scopus 로고
    • Rapid and accurate estimates of statistical significance for sequence data base searches
    • Waterman M.S., and Vingron M. Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 4625-4628
    • (1994) Proc. Natl. Acad. Sci. U. S. A. , vol.91 , pp. 4625-4628
    • Waterman, M.S.1    Vingron, M.2
  • 39
    • 0028878618 scopus 로고
    • Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
    • Wheeler W. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44 (1995) 321-331
    • (1995) Syst. Biol. , vol.44 , pp. 321-331
    • Wheeler, W.1
  • 40
    • 38549135938 scopus 로고    scopus 로고
    • Alignment uncertainty and genomic analysis
    • Wong K.M., Suchard M.A., and Huelsenbeck J.P. Alignment uncertainty and genomic analysis. Science 319 (2008) 473-476
    • (2008) Science , vol.319 , pp. 473-476
    • Wong, K.M.1    Suchard, M.A.2    Huelsenbeck, J.P.3
  • 41
    • 0032996110 scopus 로고    scopus 로고
    • Positional statistical significance in sequence alignment
    • Yu L., and Smith T.F. Positional statistical significance in sequence alignment. J. Comput. Biol. 6 (1999) 253-259
    • (1999) J. Comput. Biol. , vol.6 , pp. 253-259
    • Yu, L.1    Smith, T.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.