메뉴 건너뛰기




Volumn 546, Issue 1, 2014, Pages 25-34

K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

Author keywords

K mer model; Natural vector; Phylogenetic analysis

Indexed keywords

ARTICLE; BASE PAIRING; DNA SEQUENCE; GENE SEQUENCE; GENETIC MODEL; HUMAN; K MER NATURAL VECTOR; MATHEMATICAL ANALYSIS; MITOCHONDRIAL GENOME; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE;

EID: 84901844488     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.05.043     Document Type: Article
Times cited : (49)

References (51)
  • 2
    • 0033524478 scopus 로고    scopus 로고
    • The histidine-rich protamine from ostrich and tinamou sperm: a link between reptile and bird protamines
    • Ausio J., Soley J.T., Burger W., Lewis J.D., Barreda D., Cheng K.M. The histidine-rich protamine from ostrich and tinamou sperm: a link between reptile and bird protamines. Biochemistry 1999, 38:180-184.
    • (1999) Biochemistry , vol.38 , pp. 180-184
    • Ausio, J.1    Soley, J.T.2    Burger, W.3    Lewis, J.D.4    Barreda, D.5    Cheng, K.M.6
  • 3
    • 0032624581 scopus 로고    scopus 로고
    • Matrices, vector spaces, and information retrieval
    • Berry M.W., Drmac Z., Jessup E.R. Matrices, vector spaces, and information retrieval. SIAM Rev. 1999, 41:335-362.
    • (1999) SIAM Rev. , vol.41 , pp. 335-362
    • Berry, M.W.1    Drmac, Z.2    Jessup, E.R.3
  • 4
    • 0022743812 scopus 로고
    • A measure of the similarity of sets of sequences not requiring sequence alignment
    • Blaisdell B.E. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. U. S. A. 1986, 83:5155-5159.
    • (1986) Proc. Natl. Acad. Sci. U. S. A. , vol.83 , pp. 5155-5159
    • Blaisdell, B.E.1
  • 6
    • 0029998015 scopus 로고    scopus 로고
    • Protein sequences indicate that turtles branched off from the amniote tree after mammals
    • Caspers G.J., Reinders G.J., Leunissen J.A., Wattel J., Dejong W.W. Protein sequences indicate that turtles branched off from the amniote tree after mammals. J. Mol. Evol. 1996, 42:580-586.
    • (1996) J. Mol. Evol. , vol.42 , pp. 580-586
    • Caspers, G.J.1    Reinders, G.J.2    Leunissen, J.A.3    Wattel, J.4    Dejong, W.W.5
  • 9
    • 79952303267 scopus 로고    scopus 로고
    • A novel method of characterizing genetic sequences: genome space with biological distance and applications
    • Deng M., Yu C., Liang Q., He R.L., Yau S.S. A novel method of characterizing genetic sequences: genome space with biological distance and applications. PLoS One 2011, 6:e17293.
    • (2011) PLoS One , vol.6
    • Deng, M.1    Yu, C.2    Liang, Q.3    He, R.L.4    Yau, S.S.5
  • 10
    • 0027500136 scopus 로고
    • Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis
    • Dixon M.T., Hillis D.M. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol. Biol. Evol. 1993, 10:256-267.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 256-267
    • Dixon, M.T.1    Hillis, D.M.2
  • 11
    • 0023783671 scopus 로고
    • MHC polymorphism pre-dating speciation
    • Figueroa F., Gunther E., Klein J. MHC polymorphism pre-dating speciation. Nature 1988, 335:265-267.
    • (1988) Nature , vol.335 , pp. 265-267
    • Figueroa, F.1    Gunther, E.2    Klein, J.3
  • 14
    • 0028355535 scopus 로고
    • Molecular evidence for the origin of birds
    • Hedges S.B. Molecular evidence for the origin of birds. Proc. Natl. Acad. Sci. U. S. A. 1994, 91:2621-2624.
    • (1994) Proc. Natl. Acad. Sci. U. S. A. , vol.91 , pp. 2621-2624
    • Hedges, S.B.1
  • 15
    • 0025133472 scopus 로고
    • Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequence and a review of the evidence for amniote relationships
    • Hedges S.B., Moberg K.D., Maxson L.R. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequence and a review of the evidence for amniote relationships. Mol. Biol. Evol. 1990, 7:607-633.
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 607-633
    • Hedges, S.B.1    Moberg, K.D.2    Maxson, L.R.3
  • 16
    • 79955974855 scopus 로고    scopus 로고
    • Alignment-free comparison of genome sequences by a new numerical characterization
    • Huang G., Zhou H., Li Y.F., Xu L. Alignment-free comparison of genome sequences by a new numerical characterization. J. Theor. Biol. 2011, 281:107-112.
    • (2011) J. Theor. Biol. , vol.281 , pp. 107-112
    • Huang, G.1    Zhou, H.2    Li, Y.F.3    Xu, L.4
  • 18
    • 0034619822 scopus 로고    scopus 로고
    • Mitochondrial genome variation and the origin of modern humans
    • Ingman M., Kaessmann H., Pääbo S., Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature 2000, 408:708-713.
    • (2000) Nature , vol.408 , pp. 708-713
    • Ingman, M.1    Kaessmann, H.2    Pääbo, S.3    Gyllensten, U.4
  • 19
    • 0030778833 scopus 로고    scopus 로고
    • The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles)
    • Janke A., Arnason U. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol. Biol. Evol. 1997, 14:1266-1272.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1266-1272
    • Janke, A.1    Arnason, U.2
  • 20
    • 0028895702 scopus 로고
    • Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
    • Jermann R.M., Opitz J.G., Stackhouse J., Benner S.A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 1995, 374:57-59.
    • (1995) Nature , vol.374 , pp. 57-59
    • Jermann, R.M.1    Opitz, J.G.2    Stackhouse, J.3    Benner, S.A.4
  • 21
    • 76249122016 scopus 로고    scopus 로고
    • Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution
    • Jun S.R., Sims G.E., Wu G.A., Kim S.H. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:133-138.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 133-138
    • Jun, S.R.1    Sims, G.E.2    Wu, G.A.3    Kim, S.H.4
  • 22
    • 34547844142 scopus 로고    scopus 로고
    • A statistical method for alignment-free comparison of regulatory sequences
    • Kantorovitz M.R., Robinson G.E., Sinha S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 2007, 23:i249-i255.
    • (2007) Bioinformatics , vol.23
    • Kantorovitz, M.R.1    Robinson, G.E.2    Sinha, S.3
  • 23
    • 73949129331 scopus 로고    scopus 로고
    • Applying word-based algorithms: the IMEter
    • Korf I.F., Rose A.B. Applying word-based algorithms: the IMEter. Methods Mol. Biol. 2009, 553:287-301.
    • (2009) Methods Mol. Biol. , vol.553 , pp. 287-301
    • Korf, I.F.1    Rose, A.B.2
  • 24
    • 33748068074 scopus 로고    scopus 로고
    • Housekeeping genes for phylogenetic analysis of eutherian relationships
    • Kullberg M., Nilsson M., Arnason U., Harley E.H., Janke A. Housekeeping genes for phylogenetic analysis of eutherian relationships. Mol. Biol. Evol. 2006, 23:1493-1503.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1493-1503
    • Kullberg, M.1    Nilsson, M.2    Arnason, U.3    Harley, E.H.4    Janke, A.5
  • 26
    • 11944249445 scopus 로고
    • Geographic origins of human mitochondrial DNA: phylogenetic evidence from control region sequences
    • Maddison D.R., Ruvolo M., Swofford D.L. Geographic origins of human mitochondrial DNA: phylogenetic evidence from control region sequences. Syst. Biol. 1992, 41:111-124.
    • (1992) Syst. Biol. , vol.41 , pp. 111-124
    • Maddison, D.R.1    Ruvolo, M.2    Swofford, D.L.3
  • 27
    • 0030458552 scopus 로고    scopus 로고
    • Phylogenetic analysis in molecular evolutionary genetic
    • Nei M. Phylogenetic analysis in molecular evolutionary genetic. Annu. Rev. Genet. 1996, 30:371-403.
    • (1996) Annu. Rev. Genet. , vol.30 , pp. 371-403
    • Nei, M.1
  • 28
    • 0021028363 scopus 로고
    • Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop
    • Olivio P.D., VandeWalle M.J., Laipis P.J., Hauswirth W.W. Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop. Nature 1983, 306:400-402.
    • (1983) Nature , vol.306 , pp. 400-402
    • Olivio, P.D.1    VandeWalle, M.J.2    Laipis, P.J.3    Hauswirth, W.W.4
  • 29
    • 0028280685 scopus 로고
    • Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family
    • Ota T., Nei M. Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. Mol. Biol. Evol. 1994, 11:469-482.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 469-482
    • Ota, T.1    Nei, M.2
  • 30
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: a k-string comparison approach
    • Qi J., Wang B., Hao B.L. Whole proteome prokaryote phylogeny without sequence alignment: a k-string comparison approach. J. Mol. Evol. 2004, 58:1-11.
    • (2004) J. Mol. Evol. , vol.58 , pp. 1-11
    • Qi, J.1    Wang, B.2    Hao, B.L.3
  • 32
    • 0026660413 scopus 로고
    • A simple method for estimating and testing minimum-evolution tree
    • Rzhetsky A., Nei M. A simple method for estimating and testing minimum-evolution tree. Mol. Biol. Evol. 1992, 9:945-967.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 945-967
    • Rzhetsky, A.1    Nei, M.2
  • 33
    • 0028348061 scopus 로고
    • Evolution of the WANCY region in amniote mitochondrial DNA
    • Seutin G., Lang B.F., Mindell D.P., Morais R. Evolution of the WANCY region in amniote mitochondrial DNA. Mol. Biol. Evol. 1994, 11:329-340.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 329-340
    • Seutin, G.1    Lang, B.F.2    Mindell, D.P.3    Morais, R.4
  • 34
    • 62449130191 scopus 로고    scopus 로고
    • Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
    • Sims G.E., Jun S.R., Wu G.A., Kim S.H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:2677-2682.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 2677-2682
    • Sims, G.E.1    Jun, S.R.2    Wu, G.A.3    Kim, S.H.4
  • 35
    • 70350131711 scopus 로고    scopus 로고
    • Whole-genome phylogeny of mammals: evolutionary information in genic and non-genic regions
    • Sims G.E., Jun S.R., Wu G.A., Kim S.H. Whole-genome phylogeny of mammals: evolutionary information in genic and non-genic regions. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:17077-17082.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 17077-17082
    • Sims, G.E.1    Jun, S.R.2    Wu, G.A.3    Kim, S.H.4
  • 36
    • 13244291460 scopus 로고    scopus 로고
    • An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan linkage
    • Stuart G.W., Berry M.W. An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan linkage. BMC Bioinforma. 2004, 5:204.
    • (2004) BMC Bioinforma. , vol.5 , pp. 204
    • Stuart, G.W.1    Berry, M.W.2
  • 37
    • 0036213976 scopus 로고    scopus 로고
    • A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes
    • Stuart G.W., Moffett K., Leader J.J. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol. Biol. Evol. 2002, 19:554-562.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 554-562
    • Stuart, G.W.1    Moffett, K.2    Leader, J.J.3
  • 38
    • 0027459098 scopus 로고
    • Allelic genealogy and human evolution
    • Takahata N. Allelic genealogy and human evolution. Mol. Biol. Evol. 1993, 10:2-22.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 2-22
    • Takahata, N.1
  • 39
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10:512-526.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 40
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 41
    • 71849120074 scopus 로고    scopus 로고
    • A 2D graphical representation of protein sequence and its numerical characterization
    • Wen J., Zhang Y.Y. A 2D graphical representation of protein sequence and its numerical characterization. Chem. Phys. Lett. 2009, 476:281-286.
    • (2009) Chem. Phys. Lett. , vol.476 , pp. 281-286
    • Wen, J.1    Zhang, Y.Y.2
  • 42
    • 0027225772 scopus 로고
    • Lens crystallins: gene recruitment and evolutionary dynamism
    • Wistow G. Lens crystallins: gene recruitment and evolutionary dynamism. Trends Biochem. Sci. 1993, 18:301-306.
    • (1993) Trends Biochem. Sci. , vol.18 , pp. 301-306
    • Wistow, G.1
  • 43
    • 0031437248 scopus 로고    scopus 로고
    • A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words
    • Wu T.J., Burke J.P., Davison D.B. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics 1997, 53:1431-1439.
    • (1997) Biometrics , vol.53 , pp. 1431-1439
    • Wu, T.J.1    Burke, J.P.2    Davison, D.B.3
  • 44
    • 0035013276 scopus 로고    scopus 로고
    • Statistical measures of DNA dissimilarity under Markov chain models of base composition
    • Wu T.J., Hsieh Y.C., Li L.A. Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics 2001, 57:441-448.
    • (2001) Biometrics , vol.57 , pp. 441-448
    • Wu, T.J.1    Hsieh, Y.C.2    Li, L.A.3
  • 45
    • 27944434972 scopus 로고    scopus 로고
    • Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences
    • Wu T.J., Huang Y.H., Li L.A. Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences. Bioinformatics 2005, 21:4125-4132.
    • (2005) Bioinformatics , vol.21 , pp. 4125-4132
    • Wu, T.J.1    Huang, Y.H.2    Li, L.A.3
  • 46
    • 0038487293 scopus 로고    scopus 로고
    • 18S ribosomal RNA and tetrapod phylogeny
    • Xia X., Xie Z., Kjer K.M. 18S ribosomal RNA and tetrapod phylogeny. Syst. Biol. 2003, 52:283-295.
    • (2003) Syst. Biol. , vol.52 , pp. 283-295
    • Xia, X.1    Xie, Z.2    Kjer, K.M.3
  • 47
    • 84870524504 scopus 로고    scopus 로고
    • A novel statistical measure for sequence comparison on the basis of k-word counts
    • Yang X.W., Wang T.M. A novel statistical measure for sequence comparison on the basis of k-word counts. J. Theor. Biol. 2013, 318:91-100.
    • (2013) J. Theor. Biol. , vol.318 , pp. 91-100
    • Yang, X.W.1    Wang, T.M.2
  • 48
    • 84875382083 scopus 로고    scopus 로고
    • Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences
    • Yu H.J. Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences. Gene 2013, 518:419-424.
    • (2013) Gene , vol.518 , pp. 419-424
    • Yu, H.J.1
  • 49
    • 19944366976 scopus 로고    scopus 로고
    • Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from whole genome without sequence alignment
    • Yu Z.G., Zhou L.Q., Anh V., Chu K.H., Long S.C., Deng J.Q. Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from whole genome without sequence alignment. J. Mol. Evol. 2005, 60:538-545.
    • (2005) J. Mol. Evol. , vol.60 , pp. 538-545
    • Yu, Z.G.1    Zhou, L.Q.2    Anh, V.3    Chu, K.H.4    Long, S.C.5    Deng, J.Q.6
  • 50
    • 77955944760 scopus 로고    scopus 로고
    • A novel construction of genome space with biological geometry
    • Yu C., Liang Q., Yin C., He R.L., Yau S.S. A novel construction of genome space with biological geometry. DNA Res. 2010, 17:155-168.
    • (2010) DNA Res. , vol.17 , pp. 155-168
    • Yu, C.1    Liang, Q.2    Yin, C.3    He, R.L.4    Yau, S.S.5
  • 51
    • 0032564364 scopus 로고    scopus 로고
    • Complete mitochondrial genome suggests diapsid affinities of turtles
    • Zardoya R., Meyer A. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:14226-14231.
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 14226-14231
    • Zardoya, R.1    Meyer, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.