Towards pathogenomics: A web-based resource for pathogenicity islands

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Yoon, Sung Ho ^a   Park, Young Kyu ^a   Lee, Soohyun ^a   Choi, Doil ^a   Oh, Tae Kwang ^a   Hur, Cheol Goo ^a   Kim, Jihyun F ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; COMPUTER INTERFACE; CONTROLLED STUDY; GENBANK; GENE LOCUS; GENETIC DATABASE; GENETIC DISORDER; GENETIC SIMILARITY; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; ONLINE ANALYSIS; PATHOGENICITY; PATHOGENICITY ISLAND; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; SEQUENCE ANALYSIS;

BACTERIA; DATABASES, NUCLEIC ACID; GENOME, BACTERIAL; GENOMIC ISLANDS; GENOMICS; INTERNET; USER-COMPUTER INTERFACE; VIRULENCE FACTORS;

PROKARYOTA;

EID: 33846087685     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl790     Document Type: Article

References (29)

1. Schmidt,H. and Hensel,M. (2004) Pathogenicity islands in bacterial pathogenesis. Clin. Microbiol. Rev., 17, 14-56.
2. Nakamura,Y., Itoh,T., Matsuda,H. and Gojobori,T. (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genet., 36, 760-766.
3. Dobrindt,U., Hochhut,B., Hentschel,U. and Hacker,J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nature Rev. Microbiol., 2, 414-424.
4. Hacker,J. and Kaper,J.B. (2002) Pathogenicity Islands and The Evolution of Pathogenic Microbes. Springer-Verlag, Berlin.
5. Hacker,J., Blum-Oehler,G., Muhldorfer,I. and Tschape,H. (1997) Pathogenicity islands of virulent bacteria: Structure, function and impact on microbial evolution. Mol. Microbiol., 23, 1089-1097.
6. Hacker,J., Hochhut,B., Middendorf,B., Schneider,G., Buchrieser,C., Gottschalk,G. and Dobrindt,U. (2004) Pathogenomics of mobile genetic elements of toxigenic bacteria. Int. J. Med. Microbiol., 293, 453-461.
7. Karlin,S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol., 9, 335-343.
8. Lio,P. and Vannucci,M. (2000) Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics, 16, 932-940.
9. Tu,Q. and Ding,D. (2003) Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol. Lett., 221, 269-275.
10. Yoon,S.H., Hur,C.G., Kang,H.Y., Kim,Y.H., Oh,T.K. and Kim,J.F. (2005) A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics, 6, 184.
11. Fraser,C.M. and Rappuoli,R. (2005) Application of microbial genomic science to advanced therapeutics. Annu. Rev. Med., 56, 459-474.
12. Pompe,S., Simon,J., Wiedemann,P.M. and Tannert,C. (2005) Future trends and challenges in pathogenomics. A Foresight study. EMBO Rep., 6, 600-605.
13. Crossman,L., Cerdeno-Tarraga,A., Bentley,S. and Parkhill,J. (2003) Pathogenomics. Nature Rev. Microbiol., 1, 176-177.
14. Garcia-Vallve,S., Guzman,E., Montero,M.A. and Romeu,A. (2003) HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res., 31, 187-189.
15. Mantri,Y. and Williams,K.P. (2004) Islander: A database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res., 32, D55-D58.
16. Hsiao,W., Wan,I., Jones,S.J. and Brinkman,F.S. (2003) IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics, 19, 418-420.
17. Siguier,P., Perochon,J., Lestrade,L., Mahillon,J. and Chandler,M. (2006) ISfinder: The reference centre for bacterial insertion sequences. Nucleic Acids Res., 34, D32-D36.
18. Leplae,R., Hebrant,A., Wodak,S.J. and Toussaint,A. (2004) ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Res., 32, D45-D49.
19. Chen,L., Yang,J., Yu,J., Yao,Z., Sun,L., Shen,Y. and Jin,Q. (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res., 33, D325-D328.
20. Lawrence,J.G. and Ochman,H. (1997) Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol., 44, 383-397.
21. Kaper,J.B. and Hacker,J. (1999) Pathogenicity Islands and Other Mobile Virulence Elements. American Society for Microbiology Press, Washington, DC.
22. Hiramatsu,K., Cui,L., Kuroda,M. and Ito,T. (2001) The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends Microbiol., 9, 486-493.
23. Boyd,E.F., Moyer,K.E., Shi,L. and Waldor,M.K. (2000) Infectious CTXφ and the vibrio pathogenicity island prophage in Vibrio mimicus: Evidence for recent horizontal transfer between V.mimicus and V.cholerae. Infect. Immun., 68, 1507-1513.
24. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
25. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
26. Jeong,H., Yim,J.H., Lee,C., Choi,S.H., Park,Y.K., Yoon,S.H., Hur,C.G., Kang,H.Y., Kim,D., Lee,H.H. et al. (2005) Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res., 33, 7066-7073.
27. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
28. Holden,M., Crossman,L., Cerdeno-Tarraga,A. and Parkhill,J. (2004) Pathogenomics of non-pathogens. Nat. Rev. Microbiol., 2, 91.
29. Underwood,A.P., Mulder,A., Gharbia,S. and Green,J. (2005) Virulence Searcher: A tool for searching raw genome sequences from bacterial genomes for putative virulence factors. Clin. Microbiol. Infect., 11, 770-772.