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Nucleic Acids Res. 2015 Jan;43(Database issue):D624-30. doi: 10.1093/nar/gku985. Epub 2014 Oct 21.

PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.

Author information

1
Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea Bio-Medical Science Co., Ltd., Daejeon 305-301, Republic of Korea moncher@kribb.re.kr.
2
Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea.
3
Biosystems and Bioengineering Program, Korea University of Science and Technology, Daejeon 305-350, Republic of Korea.

Abstract

Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. Pathogenicity islands (PAIs) and resistance islands (REIs) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. While PAIs promote disease development, REIs give a fitness advantage to the host against multiple antimicrobial agents. The Pathogenicity Island Database (PAIDB, http://www.paidb.re.kr) has been the only database dedicated to providing comprehensive information on all reported PAIs and candidate PAIs in prokaryotic genomes. In this study, we present PAIDB v2.0, whose functionality is extended to incorporate REIs. PAIDB v2.0 contains 223 types of PAIs with 1331 accessions, and 88 types of REIs with 108 accessions. With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs. With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and non-pathogenic organisms.

PMID:
25336619
PMCID:
PMC4384037
DOI:
10.1093/nar/gku985
[Indexed for MEDLINE]
Free PMC Article

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