title: StaphyloBase: a specialized genomic resource for the staphylococcal research community.
abstract: With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.
authors.affiliation: Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Software Engineering, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia and Department of Computer System and Technology, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Hamed
authors.initials: H
authors.lastname: Heydari
authors.forename: Naresh V R
authors.initials: NV
authors.lastname: Mutha
authors.forename: Mahafizul Imran
authors.initials: MI
authors.lastname: Mahmud
authors.forename: Cheuk Chuen
authors.initials: CC
authors.lastname: Siow
authors.forename: Wei Yee
authors.initials: WY
authors.lastname: Wee
authors.forename: Guat Jah
authors.initials: GJ
authors.lastname: Wong
authors.forename: Amir Hessam
authors.initials: AH
authors.lastname: Yazdi
authors.forename: Mia Yang
authors.initials: MY
authors.lastname: Ang
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
mesh_terms: D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D020407:Internet; D012106:Research; D057386:Search Engine; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013210:Staphylococcus / Q000235:genetics*