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Protocols

LS-BSR specifications

Information


Unique identifier OMICS_09493
Name LS-BSR
Alternative name Large-Scale BLAST Score Ratio
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jason W. Sahl

Publication for Large-Scale BLAST Score Ratio

LS-BSR citations

 (36)
library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] qpoet (v0.3.4) using previously described primers (IntiIf: TTCGAATGTCGTAACCGC and IntiIr: CGAGGCATAGACTGTAC) and the SPAdes-assembled contigs.Accessory genomes were further explored using the program LS-BSR to determine the relative level of relatedness among isolates of each detected coding sequence (CDS). Core sequences were excluded using the filter_BSR_variome script. Accessory CDS with BLAST […]

library_books

Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection

2018
Genome Announc
PMCID: 5854770
PMID: 29545292
DOI: 10.1128/genomeA.00072-18

[…] ) in size, with an average GC content of 67.9%. PGAP predicted 6,946 coding genes, 4 complete rrn operons, and 60 tRNAs. A screen of virulence genes previously identified in B. pseudomallei using the large-scale BLAST score ratio (LS-BSR) () pipeline demonstrated the presence of the Burkholderia thailandensis-like flagellum and chemotaxis (BTFC) gene cluster (), lipopolysaccharide (LPS) genotype A […]

library_books

Piggy: a rapid, large scale pan genome analysis tool for intergenic regions in bacteria

2018
GigaScience
PMCID: 5890482
PMID: 29635296
DOI: 10.1093/gigascience/giy015

[…] ch as PanOCT and PGAP relied on all-vs-all Basic Local Alignment Search Tool (BLAST) comparisons between protein sequences and scaled approximately quadratically with the number of isolates [, ]. The large-scale blast score ratio (LS-BSR) introduced a preclustering step that substantially reduced the number of BLAST comparisons, enabling it to be feasibly run on thousands of samples []. More recen […]

library_books

Comparison of genomes and proteomes of four whole genome sequenced Campylobacter jejuni from different phylogenetic backgrounds

2018
PLoS One
PMCID: 5749857
PMID: 29293692
DOI: 10.1371/journal.pone.0190836

[…] prophages, the presence of a Type VI secretion island containing a Type VI secretion system gene cluster, and the content of hypervariable regions (Figs and ). Of the 1984 ORFs/genes identified with LS-BSR [] analysis of the 4 isolates, 626 have 100% nucleotide identity, 1500 (75.6%) are present in all isolates at a level of 90% identity or greater, 1556 (76.4%) are present at 80% identity or gre […]

library_books

Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH 21 isolated from a patient in Taiwan

2017
PMCID: 5708112
PMID: 29213333
DOI: 10.1186/s13099-017-0219-4

[…] o identify NCKUH-21 strain-specific genes, we searched the NCKUH-21 strain’s protein homologues in the genome sequences of all C. difficile strains by using the gene screen method with TBLASTN in the large-scale blast score ratio (LS-BSR) pipeline. Of the 3810 protein-coding genes identified in NCKUH-21, 3579 were conserved in all the other RT027 strains (R20291, CD196, BI1, and 2007855), and 2832 […]

library_books

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis

2017
Microb Genom
PMCID: 5695210
PMID: 29177091
DOI: 10.1099/mgen.0.000133

[…] ign DNA, we sought to investigate if the phylogenetic clusters within Y. pseudotuberculosis were associated with any signature of gene sharing. We created a pangenome matrix for all 134 genomes using LS-BSR, and then extracted the accessory genome. This accessory genome matrix was then used to annotate the core phylogenetic tree alongside CRISPR clusters (). There are clear patterns of accessory g […]

Citations

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LS-BSR institution(s)
Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA; Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA

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