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BorreliaBase: a phylogeny-centered browser of Borrelia genomes

Lia Di1, Pedro E Pagan1, Daniel Packer2, Che L Martin3, Saymon Akther1, Girish Ramrattan1, Emmanuel F Mongodin5, Claire M Fraser5, Steven E Schutzer6, Benjamin J Luft7, Sherwood R Casjens8 and Wei-Gang Qiu1349*

Author Affiliations

1 Department of Biological Sciences, Hunter College, The City University of New York, 10065 New York, NY, USA

2 Department of Computer Science, Hunter College, The City University of New York, 10065 New York, NY, USA

3 Department of Biology, The Graduate Center, City University of New York, 10016 New York, USA

4 Center for Translational and Basic Research, Hunter College, The City University of New York, 10065 New York, NY, USA

5 Institute for Genome Sciences, University of Maryland School of Medicine, 21201 Baltimore, MD, USA

6 Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, 07103 Newark, NJ, USA

7 Department of Medicine, Health Science Center, Stony Brook University, 11794 Stony Brook, NY, USA

8 Department of Pathology, Division of Molecular Cell Biology and Immunology, University of Utah School of Medicine, 84112 Salt Lake City, UT, USA

9 Department of Biological Sciences, Hunter College of the City University of New York, 695 Park Avenue, 10065 New York, NY, USA

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BMC Bioinformatics 2014, 15:233  doi:10.1186/1471-2105-15-233

Published: 3 July 2014

Abstract

Background

The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes.

Description

We have developed BorreliaBase, an online database for comparative browsing of Borrelia genomes. The database is currently populated with sequences from 35 genomes of eight Lyme-borreliosis (LB) group Borrelia species and 7 Relapsing-fever (RF) group Borrelia species. Distinct from genome repositories and aggregator databases, BorreliaBase serves manually curated comparative-genomic data including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic spacers.

Conclusions

With a genome phylogeny at its center, BorreliaBase allows online identification of hypervariable lipoprotein genes, potential regulatory elements, and recombination footprints by providing evolution-based expectations of sequence variability at each genomic locus. The phylo-centric design of BorreliaBase (http://borreliabase.org webcite) is a novel model for interactive browsing and comparative analysis of bacterial genomes online.

Keywords:
Lyme disease; Vector-borne relapsing fever; Genome browser; Recombination; Population genomics