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Volumn 28, Issue 10, 2012, Pages 1336-1344

PhyLAT: A phylogenetic local alignment tool

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; CLASSIFICATION; COMPUTER PROGRAM; DNA SEQUENCE; EVOLUTION; GENETIC DATABASE; GENETICS; GENOME; HUMAN; METHODOLOGY; OPOSSUM; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 84861143200     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts158     Document Type: Article
Times cited : (5)

References (55)
  • 1
    • 0029889221 scopus 로고    scopus 로고
    • Local alignment statistics
    • Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Meth. Enzymol., 266, 460-480.
    • (1996) Meth. Enzymol. , vol.266 , pp. 460-480
    • Altschul, S.F.1    Gish, W.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389
    • Altschul, S.F.1
  • 3
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • Altschul,S.F. et al. (2001) The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res., 29, 351.
    • (2001) Nucleic Acids Res , vol.29 , pp. 351
    • Altschul, S.F.1
  • 4
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano,G. et al. (2004) Ultraconserved elements in the human genome. Science, 304, 1321.
    • (2004) Science , vol.304 , pp. 1321
    • Bejerano, G.1
  • 6
    • 79960414804 scopus 로고    scopus 로고
    • Aligning short reads to reference alignments and trees
    • Berger,S.A. and Stamatakis,A. (2011) Aligning short reads to reference alignments and trees. Bioinformatics, 27, 15.
    • (2011) Bioinformatics , vol.27 , pp. 15
    • Berger, S.A.1    Stamatakis, A.2
  • 7
    • 79955456912 scopus 로고    scopus 로고
    • Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
    • Berger,S.A. et al. (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol., 60, 3.
    • (2011) Syst. Biol. , vol.60 , pp. 3
    • Berger, S.A.1
  • 8
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 9
    • 39049157173 scopus 로고    scopus 로고
    • Fast-evolving noncoding sequences in the human genome
    • Bird,C.P. et al. (2007) Fast-evolving noncoding sequences in the human genome. Genome Biol., 8, R118.
    • (2007) Genome Biol , vol.8
    • Bird, C.P.1
  • 10
    • 38449083186 scopus 로고    scopus 로고
    • Computation and analysis of genomic multi-sequence alignments
    • Blanchette,M. (2007) Computation and analysis of genomic multi-sequence alignments. Ann. Rev. Genom. Hum. G, 8, 193-213.
    • (2007) Ann. Rev. Genom. Hum. G , vol.8 , pp. 193-213
    • Blanchette, M.1
  • 11
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette,M. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708.
    • (2004) Genome Res , vol.14 , pp. 708
    • Blanchette, M.1
  • 12
    • 26444588761 scopus 로고    scopus 로고
    • Toward a phylogenetically aware algorithm for fast DNA similarity search
    • Buhler,J. and Nordgren,R. (2005) Toward a phylogenetically aware algorithm for fast DNA similarity search. Lect. Notes Comput. Sci., 3388, 15-29.
    • (2005) Lect. Notes Comput. Sci. , vol.3388 , pp. 15-29
    • Buhler, J.1    Nordgren, R.2
  • 13
    • 0036108574 scopus 로고    scopus 로고
    • Rapid significance estimation in local sequence alignment with gaps
    • Bundschuh,R. (2002) Rapid significance estimation in local sequence alignment with gaps. J. Comput. Biol., 9, 243-260.
    • (2002) J. Comput. Biol. , vol.9 , pp. 243-260
    • Bundschuh, R.1
  • 14
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: architecture and applications
    • Camacho,C. et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 15
    • 33748516782 scopus 로고    scopus 로고
    • On the inference of parsimonious indel evolutionary scenarios
    • Chindelevitch,L. et al. (2006) On the inference of parsimonious indel evolutionary scenarios. J. Bioinform. Comput. Biol., 4, 721-744.
    • (2006) J. Bioinform. Comput. Biol. , vol.4 , pp. 721-744
    • Chindelevitch, L.1
  • 16
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften,P. et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71.
    • (2003) Science , vol.301 , pp. 71
    • Cliften, P.1
  • 17
    • 33750371928 scopus 로고    scopus 로고
    • Finding maximum likelihood indel scenarios
    • Diallo,A.B. et al. (2006) Finding maximum likelihood indel scenarios. Lect. Notes Comput. Sci., 4205, 171.
    • (2006) Lect. Notes Comput. Sci. , vol.4205 , pp. 171
    • Diallo, A.B.1
  • 18
    • 34250354438 scopus 로고    scopus 로고
    • Exact and heuristic algorithms for the indel maximum likelihood problem
    • Diallo,A.B. et al. (2007) Exact and heuristic algorithms for the indel maximum likelihood problem. J. Comput. Biol., 14, 446-461.
    • (2007) J. Comput. Biol. , vol.14 , pp. 446-461
    • Diallo, A.B.1
  • 20
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 21
    • 44949157290 scopus 로고    scopus 로고
    • A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    • Eddy,S.R. (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol., 4, e1000069.
    • (2008) PLoS Comput. Biol. , vol.4
    • Eddy, S.R.1
  • 22
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • Eddy,S.R. et al. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2, 9-23.
    • (1995) J. Comput. Biol. , vol.2 , pp. 9-23
    • Eddy, S.R.1
  • 23
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy,S.R. et al. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
    • (2009) Genome Inform , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 24
    • 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.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792
    • Edgar, R.C.1
  • 25
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version 3.2)
    • Felsenstein,J. (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 26
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • Felsenstein,J. and Churchill,G.A. (1996) A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol., 13, 93.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 93
    • Felsenstein, J.1    Churchill, G.A.2
  • 27
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • Karlin,S. and Altschul,S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl Acad. Sci., 90, 5873.
    • (1993) Proc. Natl Acad. Sci. , vol.90 , pp. 5873
    • Karlin, S.1    Altschul, S.F.2
  • 28
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846.
    • (1998) Bioinformatics , vol.14 , pp. 846
    • Karplus, K.1
  • 29
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh,K. et al. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 14.
    • (2002) Nucleic Acids Res , vol.30 , pp. 14
    • Katoh, K.1
  • 30
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent,W.J. et al. (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 11484
    • Kent, W.J.1
  • 31
    • 33847257936 scopus 로고    scopus 로고
    • Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
    • Kim,J. and Sinha,S. (2007) Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23, 289.
    • (2007) Bioinformatics , vol.23 , pp. 289
    • Kim, J.1    Sinha, S.2
  • 32
    • 33846869288 scopus 로고    scopus 로고
    • Multiple sequence alignment: in pursuit of homologous DNA positions
    • Kumar,S. and Filipski,A. (2007) Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Res., 17, 127.
    • (2007) Genome Res. , vol.17 , pp. 127
    • Kumar, S.1    Filipski, A.2
  • 33
    • 33644876458 scopus 로고    scopus 로고
    • TreeFam: a curated database of phylogenetic trees of animalgene families
    • Li,H. et al. (2006) TreeFam: a curated database of phylogenetic trees of animalgene families. Nucleic Acids Res., 34, D572-D580.
    • (2006) Nucleic Acids Res. , vol.34
    • Li, H.1
  • 34
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison,W.P. (1997) Gene trees in species trees. Syst. Biol., 46, 3.
    • (1997) Syst. Biol. , vol.46 , pp. 3
    • Maddison, W.P.1
  • 35
    • 84874446279 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen,F. et al. (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 1.
    • (2010) BMC Bioinformatics , vol.11 , pp. 1
    • Matsen, F.1
  • 36
    • 0035057511 scopus 로고    scopus 로고
    • Models of sequence evolution for DNA sequences containing gaps
    • McGuire,G. et al. (2001) Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol., 18, 481.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 481
    • McGuire, G.1
  • 37
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: finding local similarities by multiple sequence alignment
    • Morgenstern,B. et al. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290.
    • (1998) Bioinformatics , vol.14 , pp. 290
    • Morgenstern, B.1
  • 38
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: a novel method for fast and accurate multiple sequence alignment
    • Notredame,C. et al. (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1
  • 40
    • 34547685868 scopus 로고    scopus 로고
    • Efficiently computing the robinson-foulds metric
    • Pattengale,N.D. et al. (2007) Efficiently computing the robinson-foulds metric. J. Comput. Biol., 14, 724-735.
    • (2007) J. Comput. Biol. , vol.14 , pp. 724-735
    • Pattengale, N.D.1
  • 41
    • 65549085841 scopus 로고    scopus 로고
    • Island method for estimating the statistical significance of profileprofile alignment scores
    • Poleksic,A. (2009) Island method for estimating the statistical significance of profileprofile alignment scores. BMC Bioinformatics, 10, 112.
    • (2009) BMC Bioinformatics , vol.10 , pp. 112
    • Poleksic, A.1
  • 42
    • 29144507294 scopus 로고    scopus 로고
    • Statistics of local multiple alignments
    • Prakash,A. and Tompa,M. (2005) Statistics of local multiple alignments. Bioinformatics, 21, 344.
    • (2005) Bioinformatics , vol.21 , pp. 344
    • Prakash, A.1    Tompa, M.2
  • 43
    • 35948937459 scopus 로고    scopus 로고
    • Measuring the accuracy of genome-size multiple alignments
    • Prakash,A. and Tompa,M. (2007) Measuring the accuracy of genome-size multiple alignments. Genome Biol., 8, R124.
    • (2007) Genome Biol. , vol.8
    • Prakash, A.1    Tompa, M.2
  • 44
    • 75549089967 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: update 2010
    • Rhead,B. et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613-D619.
    • (2010) Nucleic Acids Res. , vol.38
    • Rhead, B.1
  • 45
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev,R. and Grishin,N. (2003)COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
    • (2003) J. Mol. Biol. , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 46
    • 0038438514 scopus 로고    scopus 로고
    • IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    • Schaffer,A.A. et al. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000.
    • (1999) Bioinformatics , vol.15 , pp. 1000
    • Schaffer, A.A.1
  • 47
    • 1542537849 scopus 로고    scopus 로고
    • Combining phylogenetic and hidden Markov models in biosequence analysis
    • Siepel,A. and Haussler,D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol., 11, 413-428.
    • (2004) J. Comput. Biol. , vol.11 , pp. 413-428
    • Siepel, A.1    Haussler, D.2
  • 48
    • 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
  • 49
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis,A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 21.
    • (2006) Bioinformatics , vol.22 , pp. 21
    • Stamatakis, A.1
  • 50
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura,K. and Nei,M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10, 512.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512
    • Tamura, K.1    Nei, M.2
  • 51
    • 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. et al. (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.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673
    • Thompson, J.D.1
  • 52
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne,J.L. et al. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol., 33, 114-124.
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.L.1
  • 53
    • 73649145874 scopus 로고    scopus 로고
    • POYversion 4: phylogenetic analysis using dynamic homologies
    • Varón,A. et al. (2010) POYversion 4: phylogenetic analysis using dynamic homologies. Cladistics, 26, 72-85.
    • (2010) Cladistics , vol.26 , pp. 72-85
    • Varón, A.1
  • 54
    • 34547840223 scopus 로고    scopus 로고
    • Multiple alignment by aligning alignments
    • Wheeler,T.J. and Kececioglu,J.D. (2007) Multiple alignment by aligning alignments. Bioinformatics, 23, i559.
    • (2007) Bioinformatics , vol.23
    • Wheeler, T.J.1    Kececioglu, J.D.2
  • 55
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang,Z. (1995) A space-time process model for the evolution of DNA sequences. Genetics, 139, 993.
    • (1995) Genetics , vol.139 , pp. 993
    • Yang, Z.1


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