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Open AccessArticle

VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio cholerae

1
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
2
ChunLab Inc., Seoul 06725, Korea
3
Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
4
School of Biological Sciences, Seoul National University, Seoul 08826, Korea
*
Author to whom correspondence should be addressed.
Pathogens 2019, 8(4), 261; https://doi.org/10.3390/pathogens8040261
Received: 27 September 2019 / Revised: 6 November 2019 / Accepted: 21 November 2019 / Published: 23 November 2019
(This article belongs to the Special Issue Waterborne Zoonotic Pathogens)
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. View Full-Text
Keywords: comparative genomics; database; genomic island; Vibrio cholerae comparative genomics; database; genomic island; Vibrio cholerae
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MDPI and ACS Style

Hur, Y.; Chalita, M.; Ha, S.-M.; Baek, I.; Chun, J. VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio cholerae. Pathogens 2019, 8, 261.

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