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Volumn 33, Issue 14, 2005, Pages 4563-4577

Using multiple alignments to improve seeded local alignment algorithms

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC ALGORITHM; GENOMICS; INTERMETHOD COMPARISON; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; ALGORITHM; ANIMAL; EVALUATION; HUMAN; METHODOLOGY; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE;

EID: 23844438714     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki767     Document Type: Article
Times cited : (6)

References (43)
  • 1
    • 1842667855 scopus 로고    scopus 로고
    • Characterization of evolutionary rates and constraints in three mammalian genomes
    • Cooper,G.M., Brudno,M., Stone,E.A., Dubchak,I., Batzoglou,S. and Sidow,A. (2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res., 14, 539-548.
    • (2004) Genome Res. , vol.14 , pp. 539-548
    • Cooper, G.M.1    Brudno, M.2    Stone, E.A.3    Dubchak, I.4    Batzoglou, S.5    Sidow, A.6
  • 2
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent,W.J., Baertsch,R., Hinrichs,A., Miller,W. and Haussler,D. (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484-11489.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 3
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • Pevzner,P. and Tesler,G. (2003) Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res., 13, 37-45.
    • (2003) Genome Res. , vol.13 , pp. 37-45
    • Pevzner, P.1    Tesler, G.2
  • 6
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • Hillier,L.W., Miller,W., Birney,E., Warren,W., Harsison,R.C., Ponting,C.P., Bork,P., Burt,D.W. et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
    • (2004) Nature , vol.432 , pp. 695-716
    • Hillier, L.W.1    Miller, W.2    Birney, E.3    Warren, W.4    Harsison, R.C.5    Ponting, C.P.6    Bork, P.7    Burt, D.W.8
  • 8
    • 29144439098 scopus 로고    scopus 로고
    • The ENCODE Project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. (2004), The ENCODE Project. Science 306, 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 9
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman,D.J. and Pearson,W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 12
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and more sensitive homology search
    • Ma,B., Tromp,J. and Li,M. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
    • (2002) Bioinformatics , vol.18 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 13
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-like alignment tool
    • Kent,W.J. (2002) BLAT-The BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 14
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 15
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 16
    • 10944229056 scopus 로고    scopus 로고
    • A tutorial of recent developments in the seeding of local alignment
    • Brown,D.G., Li,M. and Ma,B. (2004) A tutorial of recent developments in the seeding of local alignment. J. Bioinform. Comput. Biol., 2 819-842.
    • (2004) J. Bioinform. Comput. Biol. , vol.2 , pp. 819-842
    • Brown, D.G.1    Li, M.2    Ma, B.3
  • 18
    • 4544349273 scopus 로고    scopus 로고
    • PatternHunter II: Highly sensitive and fast homology search
    • Li,M., Ma,B., Kisman,D. and Tromp,J. (2003) PatternHunter II: Highly sensitive and fast homology search. J. Bioinform. Comput. Biol., 2, 417-439.
    • (2003) J. Bioinform. Comput. Biol. , vol.2 , pp. 417-439
    • Li, M.1    Ma, B.2    Kisman, D.3    Tromp, J.4
  • 21
    • 0842321997 scopus 로고    scopus 로고
    • Sensitivity analysis and efficient method for identifying optimal spaced seeds
    • Choi,K.P. and Zhang,L. (2004) Sensitivity analysis and efficient method for identifying optimal spaced seeds. Journal of Computer and System Sciences, 68, 22-40.
    • (2004) Journal of Computer and System Sciences , vol.68 , pp. 22-40
    • Choi, K.P.1    Zhang, L.2
  • 22
    • 35248841126 scopus 로고    scopus 로고
    • Vector seeds: An extension to spaced seeds allows substantial improvements in sensitivity and specificity
    • Budapest, Hungary, Springer-Verlag
    • Brejova,B., Brown,D.G. and Vinar,T. (2003) Vector seeds: An extension to spaced seeds allows substantial improvements in sensitivity and specificity. In Proceedings of WABI (Workshop on Algorithms in Bioinformatics), vol. 2812, Budapest, Hungary, Springer-Verlag, pp. 39-54.
    • (2003) Proceedings of WABI (Workshop on Algorithms in Bioinformatics) , vol.2812 , pp. 39-54
    • Brejova, B.1    Brown, D.G.2    Vinar, T.3
  • 23
    • 0037398368 scopus 로고    scopus 로고
    • NISC Comparative Sequencing Program. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno,M., Do,C.B., Cooper,G.M., Kim,M.F., Davydov,E., Green,E.D., Sidow,A. and Batzoglou,S. NISC Comparative Sequencing Program. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13, 721-731.
    • Genome Res. , vol.13 , 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
  • 25
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • Bray,N. and Pachter,L. (2004) MAVID: Constrained ancestral alignment of multiple sequences. Genome Res., 14, 693-699.
    • (2004) Genome Res. , vol.14 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 26
    • 8744312854 scopus 로고    scopus 로고
    • A novel method for multiple alignment of sequences with repeated and shuffled elements
    • Raphael,B., Zhi,D., Tang,H. and Pevzner,P. (2004) A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res., 14, 2336-2346.
    • (2004) Genome Res. , vol.14 , pp. 2336-2346
    • Raphael, B.1    Zhi, D.2    Tang, H.3    Pevzner, P.4
  • 27
    • 3242888285 scopus 로고    scopus 로고
    • rVista 2.0: Evolutionary analysis of transcription factor binding sites
    • Loots,G.G. and Ovcharenko,I. (2004) rVista 2.0: Evolutionary analysis of transcription factor binding sites. Nucleic Acids Res., 32, W217-W221.
    • (2004) Nucleic Acids Res. , vol.32
    • Loots, G.G.1    Ovcharenko, I.2
  • 28
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: Comparative analysis and application to exon prediction
    • Batzoglou,S., Pachter,L., Mesirov,J.P., Berger,B. and Lander,E.S. (2000) Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
    • (2000) Genome Res. , vol.10 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirov, J.P.3    Berger, B.4    Lander, E.S.5
  • 29
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17, S140-S148.
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 30
    • 0037022603 scopus 로고    scopus 로고
    • Inference of functional regions in proteins by quantification of evolutionary constraints
    • Simon,A., Stone,E.A. and Sidow,A. (2002) Inference of functional regions in proteins by quantification of evolutionary constraints. Proc. Natl Acad. Sci. USA, 99, 2912-2917.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 2912-2917
    • Simon, A.1    Stone, E.A.2    Sidow, A.3
  • 32
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 34
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura,M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 35
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein,J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 38
    • 0001457509 scopus 로고
    • Some methods for classification and analysis of multivariate observations
    • Berkeley, CA, University of California Press, Berkeley, CA
    • MacQueen,J.B. (1967) Some methods for classification and analysis of multivariate observations. In Berkeley Symposium on Mathematical Statistics and Probability, vol. 1, Berkeley, CA, University of California Press, Berkeley, CA, pp. 281-297.
    • (1967) Berkeley Symposium on Mathematical Statistics and Probability , vol.1 , pp. 281-297
    • MacQueen, J.B.1
  • 39
  • 40
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 43
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin,A. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, A.1    Altschul, S.F.2


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