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Volumn 18, Issue 5, 2011, Pages 705-728

A theoretical model for whole genome alignment

Author keywords

algorithms; combinatorics; probability; sequences

Indexed keywords

ALGORITHM; ARTICLE; DNA SEQUENCE; GENOME; MATHEMATICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; THEORETICAL MODEL;

EID: 79955809167     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0101     Document Type: Article
Times cited : (2)

References (38)
  • 1
    • 65349107123 scopus 로고    scopus 로고
    • CoCoNUT: An efficient system for the comparison and analysis of genomes
    • Abouelhoda, M., Kurtz, S., and Ohlebusch, E. 2008. CoCoNUT: an efficient system for the comparison and analysis of genomes. BMC Bioinform. 9, 476.
    • (2008) BMC Bioinform. , vol.9 , pp. 476
    • Abouelhoda, M.1    Kurtz, S.2    Ohlebusch, E.3
  • 2
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S.F., Gish, W., Miller, W., et al. 1990. Basic local alignment search tool. Mol. Biol. 215, 403-410.
    • (1990) Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3
  • 3
    • 38449083186 scopus 로고    scopus 로고
    • Computation and analysis of genomic multi-sequence alignments
    • Blanchette, M. 2007. Computation and analysis of genomic multi-sequence alignments. Annu. Rev. Genomics Hum. Genet. 8, 193-213.
    • (2007) Annu. Rev. Genomics Hum. Genet. , vol.8 , pp. 193-213
    • Blanchette, M.1
  • 5
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Bray, N., Dubchak, I., and Pachter, L. 2003. AVID: a global alignment program. Genome Res. 13, 97-102.
    • (2003) Genome Res. , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 6
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • DOI 10.1101/gr.1960404
    • Bray, N., and 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
  • 7
    • 2942603015 scopus 로고    scopus 로고
    • Fast and sensitive multiple alignment of large genomic sequences
    • Brudno, M., Chapman, M., Gottgens, B., et al. 2003. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinform. 4, 66.
    • (2003) BMC Bioinform. , vol.4 , pp. 66
    • Brudno, M.1    Chapman, M.2    Gottgens, B.3
  • 9
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • DOI 10.1101/gr.2289704
    • Darling, A.C., Mau, B., Blattner, F.R., et al. 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
  • 11
    • 63849126687 scopus 로고    scopus 로고
    • Multiple whole-genome alignments without a reference organism
    • Dubchak, I., Poliakov, A., Kislyuk, A., et al. 2009. Multiple whole-genome 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
  • 15
    • 33745667975 scopus 로고    scopus 로고
    • Chaos game representation for comparison of whole genomes
    • Joseph, J., and Sasikumar, R. 2006. Chaos game representation for comparison of whole genomes. BMC Bioinform. 7, 243.
    • (2006) BMC Bioinform. , vol.7 , pp. 243
    • Joseph, J.1    Sasikumar, R.2
  • 16
    • 0034117358 scopus 로고    scopus 로고
    • Dotlet: Diagonal plots in a Web browser
    • Junier, T., and Pagni, M. 2000. Dotlet: diagonal plots in a web browser. Bioinformatics 16, 178-179. (Pubitemid 30248596)
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 178-179
    • Junier, T.1    Pagni, M.2
  • 17
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S., Phillippy, A., Delcher, A.L., et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5, R12.
    • (2004) Genome Biol. , vol.5
    • Kurtz, S.1    Phillippy, A.2    Delcher, A.L.3
  • 18
    • 33947405723 scopus 로고    scopus 로고
    • GenomeBlast: A web tool for small genome comparison
    • Lu, G., Jiang, L., Helikar, R.M., et al. 2006. GenomeBlast: a web tool for small genome comparison. BMC Bioinform. 7, S18.
    • (2006) BMC Bioinform. , vol.7
    • Lu, G.1    Jiang, L.2    Helikar, R.M.3
  • 19
    • 55549136564 scopus 로고    scopus 로고
    • The infinite sites model of genome evolution
    • Ma, J., Ratan, A., Raney, B.J., et al. 2008. The infinite sites model of genome evolution. Proc. Nat. Acad. Sci. USA 105, 14254-14261.
    • (2008) Proc. Nat. Acad. Sci. USA , vol.105 , pp. 14254-14261
    • Ma, J.1    Ratan, A.2    Raney, B.J.3
  • 21
    • 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. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Mol. Biol. 48, 443-453.
    • (1970) Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 22
    • 0242643741 scopus 로고    scopus 로고
    • A new sequence distance measure for phylogenetic tree construction
    • DOI 10.1093/bioinformatics/btg295
    • Otu, H.H., and Sayood, K. 2003. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19, 2122-2130. (Pubitemid 37408164)
    • (2003) Bioinformatics , vol.19 , Issue.16 , pp. 2122-2130
    • Otu, H.H.1    Sayood, K.2
  • 23
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten, B., Herrero, J., Fitzgerald, K.B.S., et al. 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    Fitzgerald, K.B.S.3
  • 24
    • 33750001271 scopus 로고    scopus 로고
    • MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
    • DOI 10.1093/nar/gkl514
    • Pei, J., and Grishin, N. 2006. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res. 34, 4364-4374. (Pubitemid 44567036)
    • (2006) Nucleic Acids Research , vol.34 , Issue.16 , pp. 4364-4374
    • Pei, J.1    Grishin, N.V.2
  • 25
    • 33845682909 scopus 로고    scopus 로고
    • Multiple alignment of protein sequences with repeats and rearrangements
    • DOI 10.1093/nar/gkl511
    • Phuong, T.M., Do, C.B., Edgar, R.C., et al. 2006. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res. 34, 5932-5942. (Pubitemid 44941172)
    • (2006) Nucleic Acids Research , vol.34 , Issue.20 , pp. 5932-5942
    • Phuong, T.M.1    Do, C.B.2    Edgar, R.C.3    Batzoglou, S.4
  • 26
    • 23144450376 scopus 로고    scopus 로고
    • Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
    • DOI 10.1093/nar/gki386
    • Pohler, D., Werner, N., Steinkamp, R., et al. 2005. Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. Nucleic Acids Res. 33, W532-W534. (Pubitemid 44529977)
    • (2005) Nucleic Acids Research , vol.33
    • Pohler, D.1    Werner, N.2    Steinkamp, R.3    Morgenstern, B.4
  • 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., et al. 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
  • 28
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz, S., Kent, W.J., Smit, A., et al. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
    • (2003) Genome Res. , vol.13 , pp. 103-107
    • Schwartz, S.1    Kent, W.J.2    Smit, A.3
  • 29
    • 0000526470 scopus 로고
    • Bootstrap percolation, the Schröder numbers, and the N-kings problem
    • Shapiro, L., and Stephens, A.B. 1991. Bootstrap percolation, the Schröder numbers, and the N-kings problem. SIAM J. Discr. Math. 4, 275-280.
    • (1991) SIAM J. Discr. Math. , vol.4 , pp. 275-280
    • Shapiro, L.1    Stephens, A.B.2
  • 30
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. Mol. Biol. 147, 195-197.
    • (1981) Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 31
    • 33745632116 scopus 로고    scopus 로고
    • AuberGene - A sensitive genome alignment tool
    • DOI 10.1093/bioinformatics/btl112
    • Szklarczyk, R., and Heringa, J. 2006. AuberGenena sensitive genome alignment tool. Bioinformatics 22, 1431-1436. (Pubitemid 43985312)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1431-1436
    • Szklarczyk, R.1    Heringa, J.2
  • 32
    • 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. 1994. 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, 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 33
    • 0032891717 scopus 로고    scopus 로고
    • Transformation distances: A family of dissimilarity measures based on movements of segments
    • DOI 10.1093/bioinformatics/15.3.194
    • Varre, J.-S., Delahaye, J.-P., and Rivals, E. 1999. Transformation distances: a family of dissimilarity measures based on movements of segments. Bioinformatics 15, 194-202. (Pubitemid 29196996)
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 194-202
    • Varre, J.-S.1    Delahaye, J.-P.2    Rivals, E.3
  • 34
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: Combining multiple sequence alignment methods with T-Coffee
    • Wallace, I., Sullivan, O., Higgins, D., et al. 2006. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34, 1692-1699.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 1692-1699
    • Wallace, I.1    Sullivan, O.2    Higgins, D.3
  • 36
    • 24044535485 scopus 로고    scopus 로고
    • Efficient sorting of genomic permutations by translocation, inversion and block interchange
    • DOI 10.1093/bioinformatics/bti535
    • Yancopoulos, S., Attie, O., and Friedberg, R. 2005. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346. (Pubitemid 41222437)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3340-3346
    • Yancopoulos, S.1    Attie, O.2    Friedberg, R.3
  • 37
    • 13744253626 scopus 로고    scopus 로고
    • MAP2: Multiple alignment of syntenic genomic sequences
    • DOI 10.1093/nar/gki159
    • Ye, L., and Huang, X. 2005. MAP2: multiple alignment of syntenic genomic sequences. Nucleic Acids Res. 33, 162-170. (Pubitemid 40276938)
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 162-170
    • Ye, L.1    Huang, X.2


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