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BMC Bioinformatics. 2014 Jul 3;15:233. doi: 10.1186/1471-2105-15-233.

BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Author information

  • 1Department of Biological Sciences, Hunter College, The City University of New York, 10065 New York, NY, USA. weigang@genectr.hunter.cuny.edu.

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) is a novel model for interactive browsing and comparative analysis of bacterial genomes online.

PMID:
24994456
[PubMed - indexed for MEDLINE]
PMCID:
PMC4094996
Free PMC Article
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