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Volumn 21, Issue 9, 2011, Pages 1512-1528

Cactus: Algorithms for genome multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER GRAPHICS; CONTROLLED STUDY; GENE DUPLICATION; GENE SEQUENCE; GENETIC ALGORITHM; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SIMULATOR;

EID: 80052551536     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.123356.111     Document Type: Article
Times cited : (181)

References (32)
  • 1
    • 10944228197 scopus 로고    scopus 로고
    • Reconstructing large regions of an ancestral mammalian genome in silico
    • DOI 10.1101/gr.2800104
    • Blanchette M., Green E.D., Miller W., Haussler D. 2004a. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 14: 2412-2423. (Pubitemid 40012224)
    • (2004) Genome Research , vol.14 , Issue.12 , pp. 2412-2423
    • Blanchette, M.1    Green, E.D.2    Miller, W.3    Haussler, D.4
  • 4
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • DOI 10.1101/gr.1960404
    • Bray N., Pachter L. 2004. Mavid: Constrained ancestral alignment of multiple sequences. Genome Res 14: 693-699. (Pubitemid 38500242)
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 5
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • DOI 10.1101/gr.926603
    • Brudno M., Do C.B., Cooper G.M., Kim M.F., Davydov E., Program N.C.S., Green E.D., Sidow A., Batzoglou S. 2003a. Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-731. (Pubitemid 36511930)
    • (2003) Genome Research , vol.13 , Issue.4 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3    Kim, M.F.4    Davydov, E.5    Green, E.D.6    Sidow, A.7    Batzoglou, S.8
  • 7
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • DOI 10.1101/gr.2289704
    • Darling A.C.E., Mau B., Blattner F.R., Perna N.T. 2004. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403. (Pubitemid 39029237)
    • (2004) Genome Research , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 8
    • 77956193448 scopus 로고    scopus 로고
    • Progressive Mauve: Multiple genome alignment with gene gain, loss and rearrangement
    • doi: 10.1371/journal.pone.0011147
    • Darling A.E., Mau B., Perna N.T. 2010. progressive Mauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147. doi: 10.1371/journal.pone.0011147.
    • (2010) PLoS ONE , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 9
    • 0000262264 scopus 로고
    • A combinatorial problem
    • De Bruijn N.G. 1946. A combinatorial problem. Volkskunde 1: 758-764.
    • (1946) Volkskunde , vol.1 , pp. 758-764
    • De Bruijn, N.G.1
  • 10
    • 36549051577 scopus 로고    scopus 로고
    • Aligning multiple whole genomes with mercator and mavid
    • Dewey C.N. 2007. Aligning multiple whole genomes with mercator and mavid. Methods Mol Biol 395: 221-236.
    • (2007) Methods Mol Biol , vol.395 , pp. 221-236
    • Dewey, C.N.1
  • 11
    • 63849126687 scopus 로고    scopus 로고
    • Multiple wholegenome alignments without a reference organism
    • Dubchak I., Poliakov A., Kislyuk A., Brudno M. 2009. Multiple wholegenome alignments without a reference organism. Genome Res 19: 682-689.
    • (2009) Genome Res , vol.19 , pp. 682-689
    • Dubchak, I.1    Poliakov, A.2    Kislyuk, A.3    Brudno, M.4
  • 13
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng D.F., Doolittle R.F. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25: 351-360.
    • (1987) J Mol Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 16
    • 0026605537 scopus 로고
    • CLUSTAL V: Improved software for multiple sequence alignment
    • Higgins D.G., Bleasby A.J., Fuchs R. 1992. CLUSTAL V: Improved software for multiple sequence alignment. Comput Appl Biosci 8: 189-191.
    • (1992) Comput Appl Biosci , vol.8 , pp. 189-191
    • Higgins, D.G.1    Bleasby, A.J.2    Fuchs, R.3
  • 17
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee C., Grasso C., Sharlow M.F. 2002. Multiple sequence alignment using partial order graphs. Bioinformatics 18: 452-464. (Pubitemid 34284947)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 19
    • 70349204183 scopus 로고    scopus 로고
    • Maximum likelihood genome assembly
    • Medvedev P., Brudno M. 2009. Maximum likelihood genome assembly. J Comput Biol 16: 1101-1116.
    • (2009) J Comput Biol , vol.16 , pp. 1101-1116
    • Medvedev, P.1    Brudno, M.2
  • 21
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • doi: 10.1371/journal.pcbi.0030123
    • Notredame C. 2007. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 3: e123. doi: 10.1371/journal.pcbi.0030123.
    • (2007) PLoS Comput Biol , vol.3
    • Notredame, C.1
  • 22
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten B., Herrero J., Beal K., Fitzgerald S., Birney E. 2008. Enredo and pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 18: 1814-1828.
    • (2008) Genome Res , vol.18 , pp. 1814-1828
    • Paten, B.1    Herrero, J.2    Beal, K.3    Fitzgerald, S.4    Birney, E.5
  • 23
    • 59549102237 scopus 로고    scopus 로고
    • Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    • Paten B., Herrero J., Beal K., Birney E. 2009. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics 25: 295-301.
    • (2009) Bioinformatics , vol.25 , pp. 295-301
    • Paten, B.1    Herrero, J.2    Beal, K.3    Birney, E.4
  • 26
    • 4644275238 scopus 로고    scopus 로고
    • De novo repeat classification and fragment assembly
    • DOI 10.1101/gr.2395204
    • Pevzner P.A., Pevzner P.A., Tang H., Tesler G. 2004. De novo repeat classification and fragment assembly. Genome Res 14: 1786-1796. (Pubitemid 39276437)
    • (2004) Genome Research , vol.14 , Issue.9 , pp. 1786-1796
    • Pevzner, P.A.1    Tang, H.2    Tesler, G.3
  • 27
    • 8744312854 scopus 로고    scopus 로고
    • A novel method for multiple alignment of sequences with repeated and shuffled elements
    • DOI 10.1101/gr.2657504
    • Raphael B., Zhi D., Tang H., Pevzner P. 2004. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res 14: 2336-2346. (Pubitemid 39517341)
    • (2004) Genome Research , vol.14 , Issue.11 , pp. 2336-2346
    • Raphael, B.1    Zhi, D.2    Tang, H.3    Pevzner, P.4
  • 29
    • 33846659941 scopus 로고    scopus 로고
    • Multiple alignment by sequence annealing
    • Schwartz AS, Pachter L. 2007. Multiple alignment by sequence annealing. Bioinformatics 23: e24-e29.
    • (2007) Bioinformatics , vol.23
    • Schwartz, A.S.1    Pachter, L.2
  • 31
    • 33846879183 scopus 로고    scopus 로고
    • A simple 3-edge-connected component algorithm
    • Tsin Y.H. 2007. A simple 3-edge-connected component algorithm. Theory Comput Syst 40: 125-142.
    • (2007) Theory Comput Syst , vol.40 , pp. 125-142
    • Tsin, Y.H.1
  • 32
    • 54949104412 scopus 로고    scopus 로고
    • Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
    • doi: 10.1186/gb-2008-9-10-r147
    • Varadarajan A., Bradley R.K., Holmes I.H. 2008. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol 9: R147. doi: 10.1186/gb-2008-9-10-r147.
    • (2008) Genome Biol , vol.9
    • Varadarajan, A.1    Bradley, R.K.2    Holmes, I.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.