HelicoBase: a Helicobacter genomic resource and analysis platform

BMC Genomics

Database

Jamuna Vadivelu¹  Vellaya Rehvathy¹  Mun Fai Loke¹  Hanieh Fouladi²  Naresh VR Mutha³  Cheuk Chuen Siow³  Wei Yee Wee⁴  Shi Yang Tan⁴  Mia Yang Ang⁴  Siew Woh Choo⁴  Guat Jah Wong⁴  Hamed Heydari⁵ 

[1]Department of Medical Microbiology, Faculty of Medicine Building, University of Malaya, 50603, Kuala Lumpur, Malaysia

[2]Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400, SerdangSelangor Darul Ehsan, Malaysia

[3]Genome Informatics Research Laboratory, High Impact Research (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia

[4]Genome Informatics Research Laboratory, High Impact Research (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia

[5]Department of Oral Biology and Biomedical Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

[6]Genome Informatics Research Laboratory, High Impact Research (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia

[7]Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia

关键词: HelicoBase;    Helicobacter;    Genomic resources;    Pairwise genome comparison tool;    Pathogenomics profiling tool;    Comparative analysis;   

DOI  :  10.1186/1471-2164-15-600

 received in 2014-01-09, accepted in 2014-07-09,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundHelicobacter 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.DescriptionTo 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.ConclusionsHelicoBase 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.

【 授权许可】

CC BY   
© Choo et al.; licensee BioMed Central Ltd. 2014