Exploring genome architecture through GOV: A WWW-based gene order visualizer

Bioinformatics

Volumn 20, Issue 6, 2004, Pages 984-985

  Sakharkar, Kishore R ^a   Chow, Vincent T K ^b  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; CONTROLLED STUDY; GENBANK; GENE FUNCTION; GENE ORDER; GENE ORDER VISUALIZER; GENETIC DATABASE; GENOME ANALYSIS; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN INTERACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VIRUS GENE; VIRUS GENOME;

PROKARYOTA;

EID: 2342427969     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth046     Document Type: Article

References (16)

1. Afonso,C.L., Tulman,E.R., Lu,Z., Zsak,L., Kutish,G.F. and Rock,D.L. (2000) The genome of fowlpox virus. J. Virol., 74, 3815-3831.
2. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2003) GenBank. Nucleic Acids Res., 31, 23-27.
3. Blanchette,M., Kunisawa,T. and Sankoff,D. (1999) Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49, 193-203.
4. Boore,J.L. and Brown,W.M. (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev., 8, 668-674.
5. Frishman,D., Mokrejs,M., Kosykh,D., Kastenmuller,G., Kolesov,G., Zubrzycki,I., Gruber,C., Geier,B., Kaps,A., Albermann,K. et al. (2003) The PEDANT genome database. Nucleic Acids Res., 31, 207-211.
6. Gilley,J. and Fried,M. (1999) Extensive gene order differences within regions of conserved synteny between the Fugu and human genomes: implications for chromosomal evolution and the cloning of disease genes. Hum. Mol. Genet., 8, 1313-1320.
7. Hannenhalli,S., Chappey,C., Koonin,E.V. and Pevzner,P.A. (1995) Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics, 20, 299-311.
8. Kanehisa,M. (2002) The KEGG database. Novartis Found Symp., 247, 91-101; Discussion 101-103, 119-128, 244-252.
9. Mazumder,R., Kolaskar,A. and Seto,D. (2001) GeneOrder: comparing the order of genes in small genomes. Bioinformatics, 17, 162-166.
10. Mushegian,A.R. and Koonin,E.V. (1996) Gene order is not conserved in bacterial evolution. Trends Genet., 12, 289-290.
11. Natale,D.A., Galperin,M.Y., Tatusov,R.L. and Koonin,E.V. (2000) Using the COG database to improve gene recognition in complete genomes. Genetica, 108, 9-17.
12. Overbeek,R., Larsen,N., Pusch,G.D., D'Souza,M., Selkov,E., Jr, Kyrpides,N., Fonstein,M., Maltsev,N. and Selkov,E. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res., 28, 123-125.
13. Pal,C. and Hurst,L.D. (2003) Evidence for co-evolution of gene order and recombination rate. Nat. Genet., 33, 392-395.
14. Subramanian,G., Koonin,E.V. and Aravind,L. (2000) Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect. Immun. 68, 1633-1648.
15. Tamames,J. (2001) Evolution of gene order conservation in prokaryotes. Genome Biol., 2, Research 0020.1-Research 0020.11.
16. Turmel,M., Otis,C. and Lemieux,C. (1999) The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc. Natl Acad Sci., USA, 96, 10248-10253.