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HelicoBase: a Helicobacter genomic resource and analysis platform.
Siew Woh Choo1, Mia Yang Ang, Hanieh Fouladi
1Genome Informatics Research Laboratory, High Impact Research (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia. lchoo@um.edu.my.
BMC Genomics
|July 18, 2014
Summary
HelicoBase is a new genomic resource platform for Helicobacter bacteria, offering analysis tools for 13 species and 166 genomes. This platform aids in understanding Helicobacter taxonomy, phylogeny, and pathogenicity for better disease management.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Helicobacter bacteria are Gram-negative, helical-shaped pathogens linked to various human diseases.
- Despite extensive research and genome sequencing, a dedicated platform for Helicobacter genomic analysis is lacking.
- Comparative genomic analysis is crucial for understanding Helicobacter taxonomy, phylogeny, and pathogenicity.
Purpose of the Study:
- To develop a specialized, user-friendly central repository and analysis platform for the Helicobacter research community.
- To facilitate the analysis of the growing volume of Helicobacter genomic data, particularly comparative analyses.
- To provide insights into Helicobacter taxonomy, phylogeny, and pathogenicity for improved disease management.
Main Methods:
- Developed HelicoBase, a web-based platform hosting 13 Helicobacter species and 166 genome sequences.
- Integrated comprehensive genome annotations including gene/protein sequences, functions, and subcellular localization.
- Incorporated advanced bioinformatics tools: BLAST, VFDB BLAST, Pairwise Genome Comparison (PGC), and Pathogenomics Profiling Tool (PathoProT).
- Implemented an AJAX-based search system and JBrowse for efficient data querying and genome browsing.
Main Results:
- HelicoBase provides access to a curated collection of 166 Helicobacter genomes across 13 species.
- The platform offers diverse functionalities for querying and analyzing genomic data, including similarity searches and comparative genomics.
- JBrowse enables rapid visualization and exploration of genome sequences and annotations.
- Specialized tools like PathoProT facilitate comparative pathogenomic analysis.
Conclusions:
- HelicoBase serves as a valuable, centralized resource for Helicobacter genomic data and analysis.
- The platform empowers researchers with tools for in-depth genomic exploration and comparative studies.
- HelicoBase is accessible at http://helicobacter.um.edu.my, supporting the advancement of Helicobacter research.
