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FusoBase: an online Fusobacterium comparative genomic analysis platform

Ang MY 1 , Heydari H 1 , Jakubovics NS 2 , Mahmud MI 2 , Dutta A 2 , Wee WY 1 Show all authors , Wong GJ 1 , Mutha NV 2 , Tan SY 1 , Choo SW 3

Affiliations 

  • 1 Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, 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 and Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4BW, UK Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, 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 and Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4BW, UK
  • 2 Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, 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 and Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4BW, UK
  • 3 Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, 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 and Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4BW, UK Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia, Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, 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 and Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4BW, UK lchoo@um.edu.my
Database (Oxford), 2014;2014.
PMID: 25149689 DOI: 10.1093/database/bau082

Abstract

Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, 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 infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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