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Number of citations per year for the bioinformatics software tool vConTACT
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vConTACT specifications

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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 citations

 (5)
library_books

The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow

2018
Microb Genom
PMCID: 5885020
PMID: 29583117
DOI: 10.1099/mgen.0.000169

[…] acterium 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 b […]

library_books

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

2018
Environ Microbiol
PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] active 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) are cl […]

library_books

Deciphering the Human Virome with Single Virus Genomics and Metagenomics

2018
Viruses
PMCID: 5869506
PMID: 29509721
DOI: 10.3390/v10030113

[…] s (25,561 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) []. […]

library_books

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence based framework for family level virus classification

2018
Microbiome
PMCID: 5819261
PMID: 29458427
DOI: 10.1186/s40168-018-0422-7

[…] versity of bacterial and archaeal viruses that populate marine and other environments. Future comparative evaluation of other approaches to systematic phage and archaeal virus classification, such as vConTACT [] with bipartite methods and GRAViTy will be helpful in the future development of a combined, comprehensive classification tool that can take on the vast diversity of the virosphere. […]

library_books

Single virus genomics reveals hidden cosmopolitan and abundant viruses

2017
Nat Commun
PMCID: 5490008
PMID: 28643787
DOI: 10.1038/ncomms15892

[…] BLASTP 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 usin […]


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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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