메뉴 건너뛰기




Volumn 281, Issue 1, 2011, Pages 107-112

Alignment-free comparison of genome sequences by a new numerical characterization

Author keywords

Alignment free comparison; DNA sequence; Graphical representation; Numerical characterization; Phylogenetic tree

Indexed keywords

DNA; GENOME; NUMERICAL METHOD; PHYLOGENETICS;

EID: 79955974855     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.04.003     Document Type: Article
Times cited : (31)

References (28)
  • 1
    • 77956169760 scopus 로고    scopus 로고
    • 3D graphical representation of protein sequences and their statistical characterization
    • Abo El Maaty M.I., Abo-Elkhier M.M., Abd Elwahaab M.A. 3D graphical representation of protein sequences and their statistical characterization. Physica A 2010, 389:4668-4676.
    • (2010) Physica A , vol.389 , pp. 4668-4676
    • Abo El Maaty, M.I.1    Abo-Elkhier, M.M.2    Abd Elwahaab, M.A.3
  • 2
    • 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. USA 1986, 83:5155-5159.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 5155-5159
    • Blaisdell, B.E.1
  • 3
    • 49649087115 scopus 로고    scopus 로고
    • H-L curve: a novel 2D graphical representation for DNA sequences
    • Huang G., Liao B., Li Y., Liu Z. H-L curve: a novel 2D graphical representation for DNA sequences. Chem. Phys. Lett. 2008, 462:129-132.
    • (2008) Chem. Phys. Lett. , vol.462 , pp. 129-132
    • Huang, G.1    Liao, B.2    Li, Y.3    Liu, Z.4
  • 4
    • 65749103383 scopus 로고    scopus 로고
    • Similarity studies of DNA sequences based on a new 2D graphical representation
    • Huang G., Liao B., Li Y., Yu Y. Similarity studies of DNA sequences based on a new 2D graphical representation. Biophys. Chem. 2009, 243:55-59.
    • (2009) Biophys. Chem. , vol.243 , pp. 55-59
    • Huang, G.1    Liao, B.2    Li, Y.3    Yu, Y.4
  • 5
    • 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. USA 2010, 107:133-138.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 133-138
    • Jun, S.-R.1    Sims, G.E.2    Wu, G.A.3    Kim, S.-H.4
  • 6
    • 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, 23:249-255.
    • (2007) Bioinformatics , vol.23 , pp. 249-255
    • Kantorovitz, M.R.1    Robinson, G.E.2    Sinha, S.3
  • 7
    • 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
  • 8
    • 33746210129 scopus 로고    scopus 로고
    • A 3D graphical representation of DNA sequences and its application
    • Liao B., Ding K. A 3D graphical representation of DNA sequences and its application. Theor. Comput. Sci. 2006, 358:56-64.
    • (2006) Theor. Comput. Sci. , vol.358 , pp. 56-64
    • Liao, B.1    Ding, K.2
  • 9
    • 3142704623 scopus 로고    scopus 로고
    • New 2D graphical representation of DNA sequences
    • Liao B., Wang T.M. New 2D graphical representation of DNA sequences. J. Comput. Chem. 2004, 25:1364-1368.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1364-1368
    • Liao, B.1    Wang, T.M.2
  • 10
    • 0037195172 scopus 로고    scopus 로고
    • Distributional regimes for the number of k-word matches between two random sequences
    • Lippert R.A., Huang H., Waterman M.S. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl. Acad. Sci. USA 2002, 99:13980-13989.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 13980-13989
    • Lippert, R.A.1    Huang, H.2    Waterman, M.S.3
  • 11
    • 33749518282 scopus 로고    scopus 로고
    • Mathematical descriptors of DNA sequences: development and applications
    • Nandy A., Harle M.S., Basak C. Mathematical descriptors of DNA sequences: development and applications. ARKIVOC 2006, 9:211-238.
    • (2006) ARKIVOC , vol.9 , pp. 211-238
    • Nandy, A.1    Harle, M.S.2    Basak, C.3
  • 12
    • 36249019849 scopus 로고    scopus 로고
    • New 3D graphical representation of DNA sequence based on dual nucleotides
    • Qi X.Q., Wen J., Qi Z.H. New 3D graphical representation of DNA sequence based on dual nucleotides. J. Theor. Biol. 2007, 249:681-690.
    • (2007) J. Theor. Biol. , vol.249 , pp. 681-690
    • Qi, X.Q.1    Wen, J.2    Qi, Z.H.3
  • 14
    • 0034186712 scopus 로고    scopus 로고
    • On the similarity of DNA primary sequences
    • Randić M., Vračko M. On the similarity of DNA primary sequences. J. Chem. Inf. Comput. Sci. 2000, 40:599-606.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 599-606
    • Randić, M.1    Vračko, M.2
  • 15
    • 0034266159 scopus 로고    scopus 로고
    • On 3-D graphical representation of DNA primary sequences and their numerical characterization
    • Randić M., Vračko M., Nandy A., et al. On 3-D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inf. Comput. Sci. 2000, 40:1235-1244.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 1235-1244
    • Randić, M.1    Vračko, M.2    Nandy, A.3
  • 16
    • 0037470662 scopus 로고    scopus 로고
    • Analysis of similarity/dissimilarity of DNA sequences based on novel 2D graphical representation
    • Randić M., Vračko M., Lerš N., Plavšić D. Analysis of similarity/dissimilarity of DNA sequences based on novel 2D graphical representation. Chem. Phys. Lett. 2003, 371:202-207.
    • (2003) Chem. Phys. Lett. , vol.371 , pp. 202-207
    • Randić, M.1    Vračko, M.2    Lerš, N.3    Plavšić, D.4
  • 17
    • 0033093936 scopus 로고    scopus 로고
    • Indexing scheme and similarity measures for macromolecular sequences
    • Raychaudhury C., Nandy A. Indexing scheme and similarity measures for macromolecular sequences. J. Chem. Inf. Comput. Sci. 1999, 39:243-247.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 243-247
    • Raychaudhury, C.1    Nandy, A.2
  • 18
    • 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. USA 2009, 106:2677-2682.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 2677-2682
    • Sims, G.E.1    Jun, S.-R.2    Wu, G.A.3    Kim, S.-H.4
  • 19
    • 70350131711 scopus 로고    scopus 로고
    • Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions
    • Sims G.E., Jun S-R., Wu G.A., Kim S-H. Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc. Natl. Acad. Sci. USA 2009, 106:17077-17082.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 17077-17082
    • Sims, G.E.1    Jun, S.-R.2    Wu, G.A.3    Kim, S.-H.4
  • 20
    • 21344441498 scopus 로고    scopus 로고
    • A new 2-D graphical representation of DNA sequences and their numerical characterization
    • Song J., Tang H. A new 2-D graphical representation of DNA sequences and their numerical characterization. J. Biochem. Biophys. Methods 2005, 63:228-239.
    • (2005) J. Biochem. Biophys. Methods , vol.63 , pp. 228-239
    • Song, J.1    Tang, H.2
  • 21
    • 0036166508 scopus 로고    scopus 로고
    • Integrated gene species phylogenies from unaligned whole genome protein sequences
    • Stuart G.W., Moffet K., Baker S. Integrated gene species phylogenies from unaligned whole genome protein sequences. Bioinformatics 2002, 18:100-108.
    • (2002) Bioinformatics , vol.18 , pp. 100-108
    • Stuart, G.W.1    Moffet, K.2    Baker, S.3
  • 22
    • 0036213976 scopus 로고    scopus 로고
    • A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes
    • Stuart G.W., Moffet 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    Moffet, K.2    Leader, J.J.3
  • 23
    • 0037342499 scopus 로고    scopus 로고
    • Alignment-free sequence comparison-a review
    • Vinga S., Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19:513-523.
    • (2003) Bioinformatics , vol.19 , pp. 513-523
    • Vinga, S.1    Almeida, J.2
  • 24
    • 71849120074 scopus 로고    scopus 로고
    • A 2D graphical representation of protein sequence and its numerical characterization
    • Wen J., Zhang 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.2
  • 25
    • 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
  • 26
    • 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
  • 27
    • 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, 21:4124-4132.
    • (2005) Bioinformatics , vol.21 , pp. 4124-4132
    • Wu, T.-J.1    Huang, Y.-H.2    Li, L.-A.3
  • 28
    • 77955944760 scopus 로고    scopus 로고
    • Construction of genome space with biological geometry
    • Yu C., Liang Q., Yin C., He R.L., Yau S.S-T., Novel A 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.-T.5    Novel, A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.