title: YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.
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.
  
  
  METHODS
  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 .
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.
authors.forename: Shi Yang
authors.initials: SY
authors.lastname: Tan
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. avirupdutta@gmail.com.
authors.forename: Avirup
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom. nick.jakubovics@ncl.ac.uk.
authors.forename: Nicholas S
authors.initials: NS
authors.lastname: Jakubovics
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. angmiayang@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. angmiayang@gmail.com.
authors.forename: Mia Yang
authors.initials: MY
authors.lastname: Ang
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. cheukchuen@gmail.com.
authors.forename: Cheuk Chuen
authors.initials: CC
authors.lastname: Siow
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. nareshmvr@gmail.com.
authors.forename: Naresh Vr
authors.initials: NV
authors.lastname: Mutha
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. heydarihamed@yahoo.com.|Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia. heydarihamed@yahoo.com.
authors.forename: Hamed
authors.initials: H
authors.lastname: Heydari
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. gavinwwy89@hotmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. gavinwwy89@hotmail.com.
authors.forename: Wei Yee
authors.initials: WY
authors.lastname: Wee
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. winnie.my23dna@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. winnie.my23dna@gmail.com.
authors.forename: Guat Jah
authors.initials: GJ
authors.lastname: Wong
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. lchoo@um.edu.my.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. lchoo@um.edu.my.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
mesh_terms: D002874:Chromosome Mapping; D030541:Databases, Genetic; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D010802:Phylogeny; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D014774:Virulence / Q000235:genetics*; D015007:Yersinia / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D015009:Yersinia Infections / Q000382:microbiology