Towards pathogenomics: A web-based resource for pathogenicity islands

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

Research output: Contribution to journalArticlepeer-review

62 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)D395-D400
JournalNucleic acids research
Volume35
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 2007 Jan

Bibliographical note

Funding Information:
The authors thank Ensoltek Co., Ltd (www.ensoltek.co.kr) for help in the development of the genome map viewer. The authors also thank Seung-Hwan Park, Haeyoung Jeong and Choong-Min Ryu for comments on the work and critical reading of the manuscript. This work was financially supported by the 21C Frontier Microbial Genomics and Applications Center Program, Ministry of Science and Technology, Republic of Korea. Funding to pay the Open Access publication charges for this article was provided by the same program.

All Science Journal Classification (ASJC) codes

  • Genetics

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