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vConTACT specifications

Information


Unique identifier OMICS_22173
Name vConTACT
Alternative name Viral CONTigs Automatic Clustering and Taxonomy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some viral sequences.
Input format CSV
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Requirements
Numpy, Scipy, Biopython, Pandas
Maintained No

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Publication for Viral CONTigs Automatic Clustering and Taxonomy

vConTACT in publications

 (9)
PMCID: 5929515
PMID: 29715277
DOI: 10.1371/journal.pone.0196662

[…] three beads, i.e., phosphate(p), sugar(s), and base(b). bases were classified as two types, i.e., purine(r) and pyrimidine(y). the energy function of the rna molecule was given by vrna(r|r0)=vlocal+vcontact+vele+vexv(3) the local term vlocal includes the potentials of the virtual bond, virtual angles and virtual dihedrals formed by covalently connected beads. only the virtual angles formed […]

PMCID: 5885020
PMID: 29583117
DOI: 10.1099/mgen.0.000169

[…] and gordonia and the number of myoviridae was small, 16 in total. recently, two approaches to bacteriophage classification based on blast comparisons of bacteriophage genomes were published: vcontact [] is a re-evaluation of a gene-sharing network using more than 2000 bacteriophage genomes, while victor [] reconstructs phylogenetic trees using distance matrices obtained from transformed […]

PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] or inactive., a genome‐based classification of these prophages, based on protein clustering and network clustering as done previously (lima‐mendez et al., ; roux et al., , ), was performed using vcontact (https://bitbucket.org/mavericlab/vcontact, sig score ≥ 2, default parameters otherwise). briefly, viral genomes (complete or partial, from free‐living viruses or integrated prophages) […]

PMCID: 5869506
PMID: 29509721
DOI: 10.3390/v10030113

[…] proteins) were compared using all-versus-all blastp (e-value < 1 × 10−5), then protein clusters were defined using the markov clustering algorithm (mcl) [] with default parameters. finally, vcontact [] was used to calculate a similarity score between every pair of sequences, and the network was created using cytoscape (v.3.5.1) []., in our study, saliva was collected from three […]

PMCID: 5490008
PMID: 28643787
DOI: 10.1038/ncomms15892

[…] with an e-value threshold of 10−5 and 50 for bit score. protein clusters (pcs) were then defined using markov clustering algorithm (mcl), using default parameters and 2 for an inflation value. vcontact (https://bitbucket.org/mavericlab/vcontact) was then used to calculate a similar score between every pair of genomes based on the number of pcs shared between two sequences and all pairs […]


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vConTACT institution(s)
Department of Microbiology, Ohio State University, Columbus, OH, USA; Institut de Biologie de l’ENS (IBENS), École normale supérieure, PSL Research University, Paris, France; ESPCI, PSL Research University, Paris, France; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
vConTACT funding source(s)
Supported by awards from the US Department of Energy, Office of Science, Office of Biological and Environmental Research under the Genomic Science program (DE-SC0010580), the National Science Foundation (OCE-1536989), and the Gordon and Betty Moore Foundation (#3790, 3305) and computational resources provided by the Ohio Supercomputer Center (1987).

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