title: VibrioBase: a model for next-generation genome and annotation database development.
abstract: To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
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.
authors.forename: Hamed
authors.identifier: 0000-0001-6708-9116
authors.initials: H
authors.lastname: Heydari
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Tze King
authors.initials: TK
authors.lastname: Tan
authors.affiliation: Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Cheuk Chuen
authors.identifier: 0000-0001-8336-7059
authors.initials: CC
authors.lastname: Siow
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Ching Yew
authors.identifier: 0000-0002-3737-401X
authors.initials: CY
authors.lastname: Beh
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Wei Yee
authors.identifier: 0000-0001-8965-0680
authors.initials: WY
authors.lastname: Wee
authors.affiliation: Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Naresh V R
authors.initials: NV
authors.lastname: Mutha
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Guat Jah
authors.initials: GJ
authors.lastname: Wong
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Mia Yang
authors.identifier: 0000-0003-2709-6754
authors.initials: MY
authors.lastname: Ang
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Department of Computer System & Technology, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Amir Hessam
authors.identifier: 0000-0001-5685-9568
authors.initials: AH
authors.lastname: Yazdi
mesh_terms: D066289:Data Curation / Q000379:methods / Q000639:trends*; D030541:Databases, Genetic / Q000639:trends*; D016680:Genome, Bacterial / Q000235:genetics*; D010802:Phylogeny; D014733:Vibrio / Q000235:genetics*