Fractals related to long DNA sequences and complete genomes

被引:97
作者
Hao, BL
Lee, HC
Zhang, SY
机构
[1] Ctr Theoret Sci, Hsinchu 300, Taiwan
[2] Natl Cent Univ, Dept Phys, Chungli 320, Taiwan
[3] Natl Cent Univ, Ctr Complex Syst, Chungli 320, Taiwan
[4] Acad Sinica, Inst Phys, Beijing 100080, Peoples R China
关键词
D O I
10.1016/S0960-0779(98)00182-9
中图分类号
O1 [数学];
学科分类号
0701 ; 070101 ;
摘要
In visualizing very long DNA sequences, including the complete genomes of several bacteria, yeast and segments of human genes, we encounter fractal-like patterns underlying these biological objects of prominent importance. The method used here to visualize genomes of organisms may well be used as a convenient tool to trace, e.g., evolutionary relatedness of species. We describe the method and explain the origin of the observed fractal-like patterns. (C) 2000 Elsevier Science Ltd. All rights reserved.
引用
收藏
页码:825 / 836
页数:12
相关论文
共 22 条
[1]   Is the geometry of nature fractal? [J].
Avnir, D ;
Biham, O ;
Lidar, D ;
Malcai, O .
SCIENCE, 1998, 279 (5347) :39-40
[2]   The complete genome sequence of Escherichia coli K-12 [J].
Blattner, FR ;
Plunkett, G ;
Bloch, CA ;
Perna, NT ;
Burland, V ;
Riley, M ;
ColladoVides, J ;
Glasner, JD ;
Rode, CK ;
Mayhew, GF ;
Gregor, J ;
Davis, NW ;
Kirkpatrick, HA ;
Goeden, MA ;
Rose, DJ ;
Mau, B ;
Shao, Y .
SCIENCE, 1997, 277 (5331) :1453-+
[3]   Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii [J].
Bult, CJ ;
White, O ;
Olsen, GJ ;
Zhou, LX ;
Fleischmann, RD ;
Sutton, GG ;
Blake, JA ;
FitzGerald, LM ;
Clayton, RA ;
Gocayne, JD ;
Kerlavage, AR ;
Dougherty, BA ;
Tomb, JF ;
Adams, MD ;
Reich, CI ;
Overbeek, R ;
Kirkness, EF ;
Weinstock, KG ;
Merrick, JM ;
Glodek, A ;
Scott, JL ;
Geoghagen, NSM ;
Weidman, JF ;
Fuhrmann, JL ;
Nguyen, D ;
Utterback, TR ;
Kelley, JM ;
Peterson, JD ;
Sadow, PW ;
Hanna, MC ;
Cotton, MD ;
Roberts, KM ;
Hurst, MA ;
Kaine, BP ;
Borodovsky, M ;
Klenk, HP ;
Fraser, CM ;
Smith, HO ;
Woese, CR ;
Venter, JC .
SCIENCE, 1996, 273 (5278) :1058-1073
[4]   The complete genome of the hyperthermophilic bacterium Aquifex aeolicus [J].
Deckert, G ;
Warren, PV ;
Gaasterland, T ;
Young, WG ;
Lenox, AL ;
Graham, DE ;
Overbeek, R ;
Snead, MA ;
Keller, M ;
Aujay, M ;
Huber, R ;
Feldman, RA ;
Short, JM ;
Olsen, GJ ;
Swanson, RV .
NATURE, 1998, 392 (6674) :353-358
[5]   WHOLE-GENOME RANDOM SEQUENCING AND ASSEMBLY OF HAEMOPHILUS-INFLUENZAE RD [J].
FLEISCHMANN, RD ;
ADAMS, MD ;
WHITE, O ;
CLAYTON, RA ;
KIRKNESS, EF ;
KERLAVAGE, AR ;
BULT, CJ ;
TOMB, JF ;
DOUGHERTY, BA ;
MERRICK, JM ;
MCKENNEY, K ;
SUTTON, G ;
FITZHUGH, W ;
FIELDS, C ;
GOCAYNE, JD ;
SCOTT, J ;
SHIRLEY, R ;
LIU, LI ;
GLODEK, A ;
KELLEY, JM ;
WEIDMAN, JF ;
PHILLIPS, CA ;
SPRIGGS, T ;
HEDBLOM, E ;
COTTON, MD ;
UTTERBACK, TR ;
HANNA, MC ;
NGUYEN, DT ;
SAUDEK, DM ;
BRANDON, RC ;
FINE, LD ;
FRITCHMAN, JL ;
FUHRMANN, JL ;
GEOGHAGEN, NSM ;
GNEHM, CL ;
MCDONALD, LA ;
SMALL, KV ;
FRASER, CM ;
SMITH, HO ;
VENTER, JC .
SCIENCE, 1995, 269 (5223) :496-512
[6]   THE MINIMAL GENE COMPLEMENT OF MYCOPLASMA-GENITALIUM [J].
FRASER, CM ;
GOCAYNE, JD ;
WHITE, O ;
ADAMS, MD ;
CLAYTON, RA ;
FLEISCHMANN, RD ;
BULT, CJ ;
KERLAVAGE, AR ;
SUTTON, G ;
KELLEY, JM ;
FRITCHMAN, JL ;
WEIDMAN, JF ;
SMALL, KV ;
SANDUSKY, M ;
FUHRMANN, J ;
NGUYEN, D ;
UTTERBACK, TR ;
SAUDEK, DM ;
PHILLIPS, CA ;
MERRICK, JM ;
TOMB, JF ;
DOUGHERTY, BA ;
BOTT, KF ;
HU, PC ;
LUCIER, TS ;
PETERSON, SN ;
SMITH, HO ;
HUTCHISON, CA ;
VENTER, JC .
SCIENCE, 1995, 270 (5235) :397-403
[7]   Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi [J].
Fraser, CM ;
Casjens, S ;
Huang, WM ;
Sutton, GG ;
Clayton, R ;
Lathigra, R ;
White, O ;
Ketchum, KA ;
Dodson, R ;
Hickey, EK ;
Gwinn, M ;
Dougherty, B ;
Tomb, JF ;
Fleischmann, RD ;
Richardson, D ;
Peterson, J ;
Kerlavage, AR ;
Quackenbush, J ;
Salzberg, S ;
Hanson, M ;
vanVugt, R ;
Palmer, N ;
Adams, MD ;
Gocayne, J ;
Weidman, J ;
Utterback, T ;
Watthey, L ;
McDonald, L ;
Artiach, P ;
Bowman, C ;
Garland, S ;
Fujii, C ;
Cotton, MD ;
Horst, K ;
Roberts, K ;
Hatch, B ;
Smith, HO ;
Venter, JC .
NATURE, 1997, 390 (6660) :580-586
[8]   Molecular basis of symbiosis between Rhizobium and legumes [J].
Freiberg, C ;
Fellay, R ;
Bairoch, A ;
Broughton, WJ ;
Rosenthal, A ;
Perret, X .
NATURE, 1997, 387 (6631) :394-401
[9]   Life with 6000 genes [J].
Goffeau, A ;
Barrell, BG ;
Bussey, H ;
Davis, RW ;
Dujon, B ;
Feldmann, H ;
Galibert, F ;
Hoheisel, JD ;
Jacq, C ;
Johnston, M ;
Louis, EJ ;
Mewes, HW ;
Murakami, Y ;
Philippsen, P ;
Tettelin, H ;
Oliver, SG .
SCIENCE, 1996, 274 (5287) :546-&
[10]   Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae [J].
Himmelreich, R ;
Hilbert, H ;
Plagens, H ;
Pirkl, E ;
Li, BC ;
Herrmann, R .
NUCLEIC ACIDS RESEARCH, 1996, 24 (22) :4420-4449