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BorreliaBase specifications

Information


Unique identifier OMICS_12883
Name BorreliaBase
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.20
Maintained Yes

Documentation


Maintainer


  • person_outline Wei-Gang Qiu

Publication for BorreliaBase

BorreliaBase citations

 (4)
library_books

Primordial origin and diversification of plasmids in Lyme disease agent bacteria

2018
BMC Genomics
PMCID: 5870499
PMID: 29580205
DOI: 10.1186/s12864-018-4597-x

[…] ed genomes were identified based on clusters generated by CD-HIT. Protein sequences of partition gene clusters from 34 Borreliella and 4 relapsing-fever Borrelia genome sequences were downloaded from BorreliaBase []. Orthologous sequences were aligned with MUSCLE [, ] and concatenated with BIOALN. Gene trees were inferred using FastTree, mi-point rooted and low-support branches removed by using BI […]

library_books

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

2016
PLoS One
PMCID: 5193363
PMID: 28030649
DOI: 10.1371/journal.pone.0168994

[…] ing the B. burgdorferi B31 chromosome and two B. mayonii chromosomes using a progressive Mauve 2.4.0 alignment []. The Mauve alignment was compared to the Core Genome comparison tool available at www.borreliabase.org []. Ideograms of each annotated plasmid were generated using CViT 1.2.1 (linear) and Circos 0.69 (circular) [, ]. Silent vls cassettes were determined using BLAST 2.2.30+ [] by queryi […]

library_books

Trans Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto

2016
Sci Rep
PMCID: 4783777
PMID: 26955886
DOI: 10.1038/srep22794

[…] equenced 17 European isolates () using the Illumina MiSeq technology to compare them to fully sequenced genomes available in GenBank, the majority of these strains originated from the USA (see http://borreliabase.org/). As we aimed to infer the evolutionary history of strains, we chose to analyse the main chromosome, which contains the genetic information of the core genome. In general, the reads […]

library_books

Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferi Sensu Lato

2015
MBio
PMCID: 4453575
PMID: 25873371
DOI: 10.1128/mBio.00011-15

[…] for predicting regulatory elements. To aid future computational and experimental characterization of the genome-wide regulatory network in B. burgdorferi sensu lato, we released all IGS alignments on BorreliaBase.org, a publicly accessible online database of orthologous ORFs and IGSs in Borrelia (). The website will be periodically updated to include newly released Borrelia genomes.The statistical […]

Citations

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BorreliaBase institution(s)
Department of Biological Sciences, Hunter College, The City University of New York, New York, NY, USA; Department of Computer Science, Hunter College, The City University of New York, New York, NY, USA; Department of Biology, The Graduate Center, City University of New York, New York, NY, USA; Center for Translational and Basic Research, Hunter College, The City University of New York, New York, NY, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA; Department of Medicine, Health Science Center, Stony Brook University, Stony Brook, NY, USA; Department of Pathology, Division of Molecular Cell Biology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA; Department of Biological Sciences, Hunter College of the City University of New York, New York, NY, USA
BorreliaBase funding source(s)
This work was supported by Public Health Service grants AI107955, AI37256, AI49003 and AI30071 from the National Institute of Allergy and Infectious Diseases (NIAID), and the grant MD007599 (Hunter College) from the National Institute on Minority Health and Health Disparities (NIMHD) of the National Institutes of Health (NIH).

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