Towards pathogenomics: a web-based resource for pathogenicity islands.
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.
Yoon
Sung Ho
SH
Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea.
Park
Young-Kyu
YK
Lee
Soohyun
S
Choi
Doil
D
Oh
Tae Kwang
TK
Hur
Cheol-Goo
CG
Kim
Jihyun F
JF
D001419:Bacteria / Q000235:genetics* / Q000472:pathogenicity*; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D020407:Internet; D014584:User-Computer Interface; D037521:Virulence Factors / Q000235:genetics*
D037521:Virulence Factors