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YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, Heydari H, Wee WY, Wong GJ, Choo SW - BMC Bioinformatics (2015)

Bottom Line: 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.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.We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.

ABSTRACT

Background: Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia 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 of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia 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 of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia 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 of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

Conclusions: YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .

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Related in: MedlinePlus

Genome comparisons between different subspecies of Yersinia enterocolitica by using PGC tool. PGC plots revealed yersiniabactin only present in Yersinia enterocolitica subsp. enterocolitica. (A) Comparison between 105.5R(r) and 8081 by using PGC showed that 105.5R(r) did not map to region of yersiniabactin in 8081. (B) Comparison between Y11 and 8081 by using PGC showed that Y11 did not map to region of yersiniabactin in 8081. (C) Comparison between WA-314 by using PGC showed that WA-314 mapped to region of yersiniabactin in 8081.
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Fig5: Genome comparisons between different subspecies of Yersinia enterocolitica by using PGC tool. PGC plots revealed yersiniabactin only present in Yersinia enterocolitica subsp. enterocolitica. (A) Comparison between 105.5R(r) and 8081 by using PGC showed that 105.5R(r) did not map to region of yersiniabactin in 8081. (B) Comparison between Y11 and 8081 by using PGC showed that Y11 did not map to region of yersiniabactin in 8081. (C) Comparison between WA-314 by using PGC showed that WA-314 mapped to region of yersiniabactin in 8081.

Mentions: We further visualized the difference between the two subspecies of Y. enterocolitica by using PGC Tool with Y. enterocolitica 8081 as reference genome (Figure 5). Another draft genome, Y. enterocolitica subsp. enterocolitica WA-314 was included. The start and stop position of the operon for yersiniabactin in 8081 are 2817014 and 2841569 respectively (red circle region in the Figure 5). From the three figures generated by PGC (Figure 5), we found only WA-314 has region mapped to the region encoding yersiniabactin in 8081.Figure 5


YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, Heydari H, Wee WY, Wong GJ, Choo SW - BMC Bioinformatics (2015)

Genome comparisons between different subspecies of Yersinia enterocolitica by using PGC tool. PGC plots revealed yersiniabactin only present in Yersinia enterocolitica subsp. enterocolitica. (A) Comparison between 105.5R(r) and 8081 by using PGC showed that 105.5R(r) did not map to region of yersiniabactin in 8081. (B) Comparison between Y11 and 8081 by using PGC showed that Y11 did not map to region of yersiniabactin in 8081. (C) Comparison between WA-314 by using PGC showed that WA-314 mapped to region of yersiniabactin in 8081.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384384&req=5

Fig5: Genome comparisons between different subspecies of Yersinia enterocolitica by using PGC tool. PGC plots revealed yersiniabactin only present in Yersinia enterocolitica subsp. enterocolitica. (A) Comparison between 105.5R(r) and 8081 by using PGC showed that 105.5R(r) did not map to region of yersiniabactin in 8081. (B) Comparison between Y11 and 8081 by using PGC showed that Y11 did not map to region of yersiniabactin in 8081. (C) Comparison between WA-314 by using PGC showed that WA-314 mapped to region of yersiniabactin in 8081.
Mentions: We further visualized the difference between the two subspecies of Y. enterocolitica by using PGC Tool with Y. enterocolitica 8081 as reference genome (Figure 5). Another draft genome, Y. enterocolitica subsp. enterocolitica WA-314 was included. The start and stop position of the operon for yersiniabactin in 8081 are 2817014 and 2841569 respectively (red circle region in the Figure 5). From the three figures generated by PGC (Figure 5), we found only WA-314 has region mapped to the region encoding yersiniabactin in 8081.Figure 5

Bottom Line: 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.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.We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.

ABSTRACT

Background: Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia 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 of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia 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 of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia 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 of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

Conclusions: YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .

Show MeSH
Related in: MedlinePlus