title: HelicoBase: a Helicobacter genomic resource and analysis platform.
abstract: BACKGROUND
  Helicobacter is a genus of Gram-negative bacteria, possessing a characteristic helical shape that has been associated with a wide spectrum of human diseases. Although much research has been done on Helicobacter and many genomes have been sequenced, currently there is no specialized Helicobacter genomic resource and analysis platform to facilitate analysis of these genomes. With the increasing number of Helicobacter genomes being sequenced, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of diseases caused by Helicobacter pathogens.
  
  
  METHODS
  To facilitate the ongoing research on Helicobacter, a specialized central repository and analysis platform for the Helicobacter research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data, particularly comparative analysis. Here we present HelicoBase, a user-friendly Helicobacter resource platform with diverse functionality for the analysis of Helicobacter genomic data for the Helicobacter research communities. HelicoBase hosts a total of 13 species and 166 genome sequences of Helicobacter spp. Genome annotations such as gene/protein sequences, protein function and sub-cellular localisation are also included. Our web implementation supports diverse query types and seamless searching of annotations using an AJAX-based real-time searching system. JBrowse is also incorporated to allow rapid and seamless browsing of Helicobacter genomes and annotations. Advanced bioinformatics analysis tools consisting of standard BLAST for similarity search, VFDB BLAST for sequence similarity search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis are also included to facilitate the analysis of Helicobacter genomic data.
  
  
  CONCLUSIONS
  HelicoBase offers access to a range of genomic resources as well as tools for the analysis of Helicobacter genome data. HelicoBase can be accessed at http://helicobacter.um.edu.my.
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia. lchoo@um.edu.my.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
authors.forename: Mia Yang
authors.initials: MY
authors.lastname: Ang
authors.forename: Hanieh
authors.initials: H
authors.lastname: Fouladi
authors.forename: Shi Yang
authors.initials: SY
authors.lastname: Tan
authors.forename: Cheuk Chuen
authors.initials: CC
authors.lastname: Siow
authors.forename: Naresh V R
authors.initials: NV
authors.lastname: Mutha
authors.forename: Hamed
authors.initials: H
authors.lastname: Heydari
authors.forename: Wei Yee
authors.initials: WY
authors.lastname: Wee
authors.forename: Jamuna
authors.initials: J
authors.lastname: Vadivelu
authors.forename: Mun Fai
authors.initials: MF
authors.lastname: Loke
authors.forename: Vellaya
authors.initials: V
authors.lastname: Rehvathy
authors.forename: Guat Jah
authors.initials: GJ
authors.lastname: Wong
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D016680:Genome, Bacterial; D016998:Helicobacter / Q000235:genetics*; D020407:Internet; D016366:Open Reading Frames; D057386:Search Engine