MIRU-VNTRplus protocols

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MIRU-VNTRplus specifications

Information


Unique identifier OMICS_24291
Name MIRU-VNTRplus
Alternative name Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat plus
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A single user strain.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Thomas Weniger <>

Publications for Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat plus

MIRU-VNTRplus in pipelines

 (2)
2017
PMCID: 5402389
PMID: 28436493
DOI: 10.1038/srep46666

[…] in, and flow cytometry analysis., miru-vntr 24-locus genotyping and dna extraction from bacterial cultures were performed as previously described. a minimum spanning tree was created with the miru-vntrplus database website. miru-vntr clusters were defined as strains with identical genotyping patterns and clonal complexes by a maximum difference of two loci. genomic dna of m.tb dk9897 […]

2014
PMCID: 4289236
PMID: 25407810
DOI: 10.1186/1471-2164-15-991

[…] alignment was performed using the clc sequence viewer v7.6.1 (clc bio®, aarhus n, denmark) and visualized in bioedit v7.1.3.0 (t. hall)., a miru-vntr-based dendrogram was constructed in the public miru-vntrplus database using the dsw measure of genetic distance for tandem repeat loci [] and the unweighted pair group method with arithmetic averages (upgma) clustering method. spoligotyping […]


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MIRU-VNTRplus in publications

 (114)
PMCID: 5854261
PMID: 29543819
DOI: 10.1371/journal.pone.0193626

[…] genotypes were expressed as numerical codes representing the number of miru-vntr for each locus. lineages were individually identified using the similarity search module [] of the database miru-vntrplus (http://www.miru-vntrplus.org/miru/index.faces)[]., the tree polar arrangement was realized by the figtree program (tree figure drawing tool version 1.4.3. […]

PMCID: 5844927
PMID: 29556502
DOI: 10.3389/fvets.2018.00032

[…] the discriminatory power of a genotyping method, was determined according to the formula described by hunter and gaston ()., genetic strain lineages were predicted using online tools available from miru-vntrplus website (). a dendrogram based on 20 vntr loci was generated using the unweighted pair group method using arithmetic averages (upgma) algorithm., variable number of tandem repeat data […]

PMCID: 5840967
PMID: 29531921
DOI: 10.4103/2277-9175.225594

[…] copy numbers were obtained by comparing the band sizes with an allele naming table for each tandem repeat locus made available in microsoft excel format on the miru-vntr plus website (http://www.miru-vntrplus.org). the h37rv was used as control for allele assignation., the final result of 24-locus miru-vntr typing (miru-vntr data) is a numerical code, corresponding to the repeat number […]

PMCID: 5785791
PMID: 29370774
DOI: 10.1186/s12879-018-2968-1

[…]  ).fig. 1, we determined the main geographical lineages for the m. tuberculosis isolates by comparing the genotyped samples and the miru-vntr reference strains whose lineage is well determined in the miru-vntrplus website http://www.miru-vntrplus.org., isolates that share common genetic ancestry are referred to as genotypically clustered, a potential marker for episodes of direct tb transmission. […]

PMCID: 5772998
PMID: 29346413
DOI: 10.1371/journal.pntd.0006147

[…] in order to evaluate relatedness of the spoligotype and vntr patterns of the different samples we generated a dendogram using the upgma algorithm using the tool provided on the site http://www.miru-vntrplus.org/. the spoligotype patterns of the respective isolates were entered into the mbovis.org database. in this database each unique spoligotype pattern is named by 'sb' followed by a four […]


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MIRU-VNTRplus institution(s)
Department of Periodontology, University Hospital Munster, Munster, Germany; Molecular Mycobacteriology, Forschungszentrum Borstel, Borstel, Germany; CIIL – Center for Infection and Immunity of Lille INSERM U 1019, CNRS UMR 8204 Univ Lille Nord de France, Institut Pasteur de Lille, France
MIRU-VNTRplus funding source(s)
Supported by German Federal Ministry of Education and Research in the framework of the Network Zoonoses (grant number 01KI07124) and PathoGenomikPlus Network (grant number 0313801J).

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