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VCGIDB: A database and web resource for the genomic islands from Vibrio cholerae

Cited 2 time in Web of Science Cited 2 time in Scopus
Issue Date
2019-12
Citation
Pathogens, Vol.8 No.4, p. 261
Keywords
comparative genomicsdatabasegenomic islandVibrio cholerae
Abstract
Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.
ISSN
2076-0817
URI
https://hdl.handle.net/10371/165725
DOI
https://doi.org/10.3390/pathogens8040261
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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