YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Tan, Shi; Dutta, Avirup; Jakubovics, Nicholas; Ang, Mia; Siow, Cheuk; Mutha, Naresh; Heydari, Hamed; Wee, Wei; Wong, Guat; Choo, Siew
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: YersiniaBase -- Yersinia -- Genomic resources -- Comparative analysis; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-014-0422-y
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Yersinia is a Gram-negative bacteria that includes serious pathogens such as theYersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica . The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes ofYersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growingYersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. Description To facilitate the ongoing and future research ofYersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold theYersinia genomic data and analysis tools for theYersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendlyYersinia resource and analysis platform for the analysis ofYersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority areYersinia pestis . In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis ofYersinia genomes; (3) YersiniaTree for constructing phylogenetic tree ofYersinia . We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found inYersinia pestis andYersinia pseudotuberculosis compared to otherYersinia species, and differences betweenYersinia enterocolitica subsp.enterocolitica andYersinia enterocolitica subsp.palearctica . Conclusions YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis ofYersinia . YersiniaBase can be accessed athttp://yersinia.um.edu.my .