IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W104-W108

  Dhillon, Bhavjinder K ^a   Laird, Matthew R ^a   Shay, Julie A ^a   Winsor, Geoffrey L ^a   Lo, Raymond ^a   Nizam, Fazmin ^b   Pereira, Sheldon K ^b   Waglechner, Nicholas ^b   McArthur, Andrew G ^b   Langille, Morgan G I ^c   Brinkman, Fiona S L ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b MCMASTER UNIVERSITY   (Canada)

^c DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOMIC ISLAND; MICROBIAL GENE; MICROBIAL GENOME; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; WEB BROWSER; ARCHAEAL GENOME; BACTERIAL GENOME; COMPUTER GRAPHICS; COMPUTER PROGRAM; GENETICS; GENOMICS; INTERNET;

VIRULENCE FACTOR;

COMPUTER GRAPHICS; DRUG RESISTANCE, MICROBIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMIC ISLANDS; GENOMICS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; VIRULENCE FACTORS;

EID: 84979856828     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv401     Document Type: Article

References (20)

1. Langille, M.G.I., Hsiao, W.W.L. and Brinkman, F.S.L. (2010) Detecting genomic islands using bioinformatics approaches. Nat. Rev. Microbiol., 8, 373-382.
2. Dobrindt, U., Hochhut, B., Hentschel, U. and Hacker, J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol., 2, 414-424.
3. Hacker, J. and Carniel, E. (2001) Ecological fitness, genomic islands and bacterial pathogenicity. EMBO Rep., 2, 376-381.
4. Stephens, C. and Murray, W. (2001) Pathogen evolution: how good bacteria go bad. Curr. Biol., 11, R53-R56.
5. Ho Sui, S.J., Fedynak, A., Hsiao, W.W., Langille, M.G. and Brinkman, F.S. (2009) The association of virulence factors with genomic islands. PLoS One, 4, e8094.
6. Langille, M.G.I. and Brinkman, F.S.L. (2009) Island Viewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics, 25, 664.
7. Langille, M., Hsiao, W. and Brinkman, F. (2008) Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics, 9, 329.
8. Hsiao, W., Wan, I., Jones, S.J. and Brinkman, F.S. (2003) Island Path: aiding detection of genomic islands in prokaryotes. Bioinformatics, 19, 418-420.
9. Waack, S., Keller, O., Asper, R., Brodag, T., Damm, C., Fricke, W., Surovcik, K., Meinicke, P. and Merkl, R. (2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden markov models. BMC Bioinformatics, 7, 142.
10. Chen, L., Xiong, Z., Sun, L., Yang, J. and Jin, Q. (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res., 40, D641-D645.
11. Liu, B. and Pop, M. (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res., 37, D443-D447.
12. Dhillon, B.K., Chiu, T.A., Laird, M.R., Langille, M.G. and Brinkman, F.S. (2013) Island Viewer update: improved genomic island discovery and visualization. Nucleic Acids Res., 41, W129-W132.
13. McArthur, A.G., Waglechner, N., Nizam, F., Yan, A., Azad, M.A., Baylay, A.J., Bhullar, K., Canova, M.J., De Pascale, G., Ejim, L. et al. (2013) The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother., 57, 3348-3357.
14. Hacker, J. and Kaper, J.B. (2000) Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol., 54, 641-679.
15. Gal-Mor, O. and Finlay, B.B. (2006) Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell. Microbiol., 8, 1707-1719.
16. Wattam, A.R., Abraham, D., Dalay, O., Disz, T.L., Driscoll, T., Gabbard, J.L., Gillespie, J.J., Gough, R., Hix, D., Kenyon, R. et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591.
17. Xu, Z. and Hao, B. (2009) CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res., 37, W174.
18. Lee, C., Chen, Y.P., Yao, T., Ma, C., Lo, W., Lyu, P. and Tang, C.Y. (2013) GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene, 518, 114-123.
19. Rissman, A.I., Mau, B., Biehl, B.S., Darling, A.E., Glasner, J.D. and Perna, N.T. (2009) Reordering contigs of draft genomes using the mauve aligner. Bioinformatics, 25, 2071-2073.
20. Langille, M.G., Laird, M.R., Hsiao, W.W., Chiu, T.A., Eisen, J.A. and Brinkman, F.S. (2012) Microbe DB: a locally maintainable database of microbial genomic sequences. Bioinformatics, 28, 1947-1948.