Reconstruction of ancient genome and gene order from complete microbial genome sequences

Journal of Theoretical Biology

Volumn 239, Issue 4, 2006, Pages 494-498

  Wang, Yuhong ^a   Li, Wei ^a   Zhang, Tongtong ^a   Ding, Chuanfang ^b   Lu, Zhibin ^c   Long, Nanye ^d   Rose, John P ^e   Wang, Bi Cheng ^e   Lin, Dawei ^e  

^a JILIN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c UNIVERSITY HEALTH NETWORK   (Canada)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^e University of Georgia ^*  (United States)

Author keywords

Genome evolution; Global optimization; Microbial genome sequences; Random cost algorithm; Travel salesman problem

Indexed keywords

ANCESTRY; CORRELATION; GENETIC ALGORITHM; GENOME; MICROBIOLOGY; OPTIMIZATION; PALEONTOLOGY;

ARTICLE; CONTIG MAPPING; CORRELATION ANALYSIS; GENE FREQUENCY; GENE ORDER; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; MICROBIAL GENETICS; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PALEONTOLOGY; PHYLOGENY; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE ORDER; GENOME, BACTERIAL; MODELS, GENETIC;

EID: 33645396934     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2005.08.013     Document Type: Article

References (10)

1. A.J. Cuticchia, J. Arnold, and W.E. Timberlake The use of simulated annealing in chromosome reconstruction experiments based on binary scoring Genetics 132 1992 591 601
2. B. Efron The Jackknife, the Bootstrap, and Other Resampling Plans 1982 SIAM Philadelphia
3. M. Jünger, G. Reinelt, and G. Rinaldi The traveling salesman problem M.O. Ball T. Magnanti C.L. Monma G. Nemhauser Handbooks in Operations Research and Management Science vol. 7 1995 Elsevier Science Amsterdam 225 330
4. M. Kanehisa, and S. Goto KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 28 2000 27 30
5. MacQueen, B., 1967. Some methods for classification and analysis of multivariate observations. In: Proceedings of the Symposium on Mathematics, Statistics and Probability (Fifth), vol. 1. University of California Press, Berkeley, CA, pp. 281-297.
6. A.R. Mushegian, and E.V. Koonin Gene order is not conserved in bacterial evolution Trends Genet. 12 1996 289 290
7. K.D. Pruitt, and D.R. Maglott RefSeq and LocusLink: NCBI gene-centered resources Nucleic Acids Res. 29 2001 137 140
8. R.L. Tatusov, E.V. Koonin, and D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
9. R.L. Tatusov The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res. 29 2001 22 28
10. Yuhong Wang, and Jonathan Arnold A new fast random cost algorithm of global minimization for physical mapping Proc. Natl Acad. Sci. 91 1994 11094