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Nucleic Acids Research Advance Access originally published online on November 7, 2006
Nucleic Acids Research 2007 35(Database issue):D395-D400; doi:10.1093/nar/gkl790
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Nucleic Acids Research, 2007, Vol. 35, Database issue D395-D400
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Towards pathogenomics: a web-based resource for pathogenicity islands

Sung Ho Yoon, Young-Kyu Park1, Soohyun Lee, Doil Choi1, Tae Kwang Oh2, Cheol-Goo Hur1,* and Jihyun F. Kim*

Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea 1 Plant Genome Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea 2 21C Frontier Microbial Genomics and Applications Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea

*To whom correspondence should be addressed. Tel: +82 42 860 4412; Fax: +82 42 879 8595; Email: jfk{at}kribb.re.kr

Received May 23, 2006. Revised August 23, 2006. Accepted October 2, 2006.

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at http://www.gem.re.kr/paidb.

*Correspondence may also be addressed to Cheol-Goo Hur. Tel: +82 42 879 8560; Fax: +82 42 879 8569; Email: hurlee{at}kribb.re.kr

Present address: D. Choi, Department of Plant Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea


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