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

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 s...

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Main Authors:	Tan, Shi Yang, Dutta, Avirup, Jakubovics, Nicholas S., Ang, Mia Yang, Siow, Cheuk Chuen, Mutha, Naresh V.R., Heydari, Hamed, Wee, Wei Yee, Wong, Guat Jah, Choo, Siew Woh
Format:	Article
Published:	BioMed Central 2015
Subjects:	QA75 Electronic computers. Computer science RK Dentistry
Online Access:	http://eprints.um.edu.my/19612/ http://dx.doi.org/10.1186/s12859-014-0422-y
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spelling	my.um.eprints.196122018-10-05T05:15:05Z http://eprints.um.edu.my/19612/ YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia Tan, Shi Yang Dutta, Avirup Jakubovics, Nicholas S. Ang, Mia Yang Siow, Cheuk Chuen Mutha, Naresh V.R. Heydari, Hamed Wee, Wei Yee Wong, Guat Jah Choo, Siew Woh QA75 Electronic computers. Computer science RK Dentistry 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. BioMed Central 2015 Article PeerReviewed Tan, Shi Yang and Dutta, Avirup and Jakubovics, Nicholas S. and Ang, Mia Yang and Siow, Cheuk Chuen and Mutha, Naresh V.R. and Heydari, Hamed and Wee, Wei Yee and Wong, Guat Jah and Choo, Siew Woh (2015) YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. BMC Bioinformatics, 16 (1). p. 9. ISSN 1471-2105 http://dx.doi.org/10.1186/s12859-014-0422-y doi:10.1186/s12859-014-0422-y
institution	Universiti Malaya
building	UM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaya
content_source	UM Research Repository
url_provider	http://eprints.um.edu.my/
topic	QA75 Electronic computers. Computer science RK Dentistry
spellingShingle	QA75 Electronic computers. Computer science RK Dentistry Tan, Shi Yang Dutta, Avirup Jakubovics, Nicholas S. Ang, Mia Yang Siow, Cheuk Chuen Mutha, Naresh V.R. Heydari, Hamed Wee, Wei Yee Wong, Guat Jah Choo, Siew Woh YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
description	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.
format	Article
author	Tan, Shi Yang Dutta, Avirup Jakubovics, Nicholas S. Ang, Mia Yang Siow, Cheuk Chuen Mutha, Naresh V.R. Heydari, Hamed Wee, Wei Yee Wong, Guat Jah Choo, Siew Woh
author_facet	Tan, Shi Yang Dutta, Avirup Jakubovics, Nicholas S. Ang, Mia Yang Siow, Cheuk Chuen Mutha, Naresh V.R. Heydari, Hamed Wee, Wei Yee Wong, Guat Jah Choo, Siew Woh
author_sort	Tan, Shi Yang
title	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
title_short	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
title_full	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
title_fullStr	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
title_full_unstemmed	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
title_sort	yersiniabase: a genomic resource and analysis platform for comparative analysis of yersinia
publisher	BioMed Central
publishDate	2015
url	http://eprints.um.edu.my/19612/ http://dx.doi.org/10.1186/s12859-014-0422-y
_version_	1643691038445928448
score	13.211869

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

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