메뉴 건너뛰기




Volumn 6, Issue , 2005, Pages

DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

FRAGMENT-CHAINING ALGORITHMS; GLOBAL ALIGNMENT; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; OBJECTIVE FUNCTIONS; PAIRWISE ALIGNMENT; PROTEIN ALIGNMENT; REFERENCE DATABASE;

EID: 20444489707     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-66     Document Type: Article
Times cited : (137)

References (29)
  • 1
    • 23044525766 scopus 로고    scopus 로고
    • Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB)
    • Abdeddaïm S, Morgenstern B: Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB). Lecture Notes in Computer Science 2001, 2066:1-11.
    • (2001) Lecture Notes in Computer Science , vol.2066 , pp. 1-11
    • Abdeddaïm, S.1    Morgenstern, B.2
  • 4
    • 0024297354 scopus 로고
    • Multiple sequence alignment with hierarchical clustering
    • Corpet F: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 1988, 16:10881-10890.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 10881-10890
    • Corpet, F.1
  • 5
    • 0026668613 scopus 로고
    • Match-box: A fundamentally new algorithm for the simultaneous alignment of several protein sequences
    • Depiereux E, Feytmans E: Match-box: a fundamentally new algorithm for the simultaneous alignment of several protein sequences. CABIOS 1992, 8:501-509.
    • (1992) CABIOS , vol.8 , pp. 501-509
    • Depiereux, E.1    Feytmans, E.2
  • 7
    • 0003516147 scopus 로고    scopus 로고
    • Biological sequence analysis
    • Cambridge University Press, Cambridge, UK
    • Durbin R, Eddy SR, Krogh A, Mitchison G: Biological sequence analysis Cambridge University Press, Cambridge, UK; 1998.
    • (1998)
    • Durbin, R.1    Eddy, S.R.2    Krogh, A.3    Mitchison, G.4
  • 8
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high score accuracy and high throughput
    • Edgar R: MUSCLE: Multiple sequence alignment with high score accuracy and high throughput. Nuc Acids Res 2004, 32:1792-1797.
    • (2004) Nuc. Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 9
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • 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, 264:823-838.
    • (1996) J. Mol. Biol. , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 11
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann T, Sonnhammer EL: Quality assessment of multiple alignment programs. FEBS Letters 2002, 529:126-130.
    • (2002) FEBS Letters , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 12
  • 13
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452-464.
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 14
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 15
    • 31244432403 scopus 로고    scopus 로고
    • A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
    • Morgenstern B: A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences. Applied Mathematics Letters 2002, 15:11-16.
    • (2002) Applied Mathematics Letters , vol.15 , pp. 11-16
    • Morgenstern, B.1
  • 16
    • 3242891684 scopus 로고    scopus 로고
    • DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ
    • Morgenstern B: DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Research 2004, 32:W33-W36.
    • (2004) Nucleic Acids Research , vol.32
    • Morgenstern, B.1
  • 17
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern B, Dress A, Werner T: Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci USA 1996, 93:12098-12103.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 18
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 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, 48:443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 19
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel algorithm for multiple sequence alignment
    • Notredame C, Higgins D, Heringa J: T-Coffee: a novel algorithm for multiple sequence alignment. J Mol Biol 2000, 302:205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 22
    • 8744312854 scopus 로고    scopus 로고
    • A novel method for multiple alignment of sequences with repeated and shuffled elements
    • Raphael B, Zhi D, Tang H, Pevzner P: A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research 2004, 14:2336-2346.
    • (2004) Genome Research , vol.14 , pp. 2336-2346
    • Raphael, B.1    Zhi, D.2    Tang, H.3    Pevzner, P.4
  • 23
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye J, Evers D, Meyer F: Rose: Generating sequence families. Bioinformatics 1998, 14:157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 24
    • 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 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 Research 1994, 22:4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 25
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O: BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics 1999, 15:87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 26
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of protein sequence alignment programs
    • Thompson JD, Plewniak F, Poch O: A comprehensive comparison of protein sequence alignment programs. Nucleic Acids Research 1999, 27:2682-2690.
    • (1999) Nucleic Acids Research , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 27
    • 3042613056 scopus 로고    scopus 로고
    • Align-m - A new algorithm for multiple alignment of highly divergent sequences
    • Walle IV, Lasters I, Wyns L: Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 2004, 20:1428-1435.
    • (2004) Bioinformatics , vol.20 , pp. 1428-1435
    • Walle, I.V.1    Lasters, I.2    Wyns, L.3
  • 28
    • 16344394781 scopus 로고    scopus 로고
    • SABmark - A benchmark for sequence alignment that covers the entire known fold space
    • in press. doi: 10.1093/bioinformatics/bth493
    • Walle IV, Lasters I, Wyns L: SABmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics in press. doi: 10.1093/bioinformatics/bth493.
    • Bioinformatics
    • Walle, I.V.1    Lasters, I.2    Wyns, L.3
  • 29
    • 0023057161 scopus 로고
    • Multiple sequence alignment by consensus
    • Waterman MS: Multiple sequence alignment by consensus. Nucleic Acids Res 1986, 14:9095-9102.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 9095-9102
    • Waterman, M.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.