PLACNET statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PLACNET
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Tool usage distribution map

This map represents all the scientific publications referring to PLACNET per scientific context
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Associated diseases

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Popular tool citations

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Protocols

PLACNET specifications

Information


Unique identifier OMICS_11487
Name PLACNET
Alternative names PLAsmid Constellation NETwork, PLACNETw
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input of PLACNET is a set of contigs and one or more files with the mapping of the reads against the contigs.
Input format SAM
Output data A set of files, easily opened on Cytoscape software or other network tools.
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Beta
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Ferndo de la Cruz
  • person_outline Luis Vielva

Information


Unique identifier OMICS_11487
Name PLACNET
Alternative names PLAsmid Constellation NETwork, PLACNETw
Interface Web user interface
Restrictions to use None
Input data pair-end read datasets.
Input format GZIP FASTA
Computer skills Basic
Maintained Yes

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Documentation


Maintainers


  • person_outline Ferndo de la Cruz
  • person_outline Luis Vielva

Publications for PLAsmid Constellation NETwork

PLACNET citations

 (10)
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Draft Genome Sequence of Multidrug Resistant Escherichia coli NIVEDI P44, Isolated from a Chicken Fecal Sample in Northeast India

2018
Genome Announc
PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18
call_split See protocol

[…] ch predicted a total of 4,611 protein-coding sequences, 73 pseudogenes, 72 tRNAs, and 3 rRNA clusters. The NIVEDI-P44 strain belongs to multilocus sequence type (MLST) 746 (ST746). Plasmid Finder and PLACNET (, ) detected three plasmid sequences, viz., IncN, ColpVC, and p0111 (IncHI1). Of these, p0111 harbored the tet(A) gene (encodes tetracycline resistance). PHAST analysis () detected 3 intact p […]

library_books

mcr 1 in Carbapenemase Producing Klebsiella pneumoniae with Hospitalized Patients, Portugal, 2016–2017

2018
PMCID: 5875258
PMID: 29553327
DOI: 10.3201/eid2404.171787

[…] ith Prokka (http://vicbioinformatics.com/). We used tools from the Center for Genomic Epidemiology (http://www.genomicepidemiology.org) to assess antimicrobial drug resistance genes and replicons and PLACNETw (https://castillo.dicom.unican.es/upload/) for plasmid reconstruction. We located mcr-1 in the IncX4 plasmid near the replication (pirF) and maintenance (parA) conserved regions by PCR and se […]

library_books

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

2018
Microb Genom
PMCID: 5885016
PMID: 29533742
DOI: 10.1099/mgen.0.000164

[…] arger more complex plasmids. All of these software applications utilize SPAdes within their methods, work on a single sample at a time, and require no a priori knowledge about the samples themselves. placnet can additionally be used for plasmid reconstruction from WGS data []; however, as noted in [], the workflow includes a manual pruning step, so it was excluded from the present evaluation of fu […]

library_books

Whole genome sequencing, molecular typing and in vivo virulence of OXA 48 producing Escherichia coli isolates including ST131 H30 Rx, H22 and H41 subclones

2017
Sci Rep
PMCID: 5608912
PMID: 28935873
DOI: 10.1038/s41598-017-12015-0

[…] Plasmid reconstructions were based on the PLACNET method. Contig analysis was performed against complete bacterial genomes and plasmids from GenBank-NCBI. Relaxase proteins (REL) and Replication Initiation Proteins (RIP) were identified using […]

library_books

On the (im)possibility of reconstructing plasmids from whole genome short read sequencing data

2017
Microb Genom
PMCID: 5695206
PMID: 29177087
DOI: 10.1099/mgen.0.000128

[…] whether a previously assembled contig is from a plasmid (PlasmidFinder, cBar), or try to reconstruct whole plasmid sequences from the sequencing reads or the assembly graph (Recycler, PlasmidSPAdes, PLACNET) ().PlasmidFinder is a web-based tool that was developed to detect replicon sequences in assemblies and is optimized for use in enterobacterial genomes []. Since two plasmids sharing the same […]

library_books

Population Genomics of Legionella longbeachae and Hidden Complexities of Infection Source Attribution

2017
PMCID: 5403047
PMID: 28418314
DOI: 10.3201/eid2305.161165

[…] o contain plasmids with sequences homologous to those for pLLO and pLELO, which is indicative of recombinant forms of the plasmid. Further examination of plasmid diversity using a modified version of PLACNET (), a program enabling reconstruction of plasmids from whole-genome sequence datasets, confirmed that some plasmids consisted of a mosaic of recombinant fragments homologous to pLELO, pLLO, or […]


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PLACNET institution(s)
Departamento de Ingeniería de Comunicaciones, Universidad de Cantabria, Santander, Spain; Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain; Departamento de Microbiología, Instituto de Investigación Sanitaria Ramón y Cajal (IRYCIS), Madrid, Spain; Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria- CSIC), Santander, Spain
PLACNET funding source(s)
Supported by the Spanish Ministry of Economy and Competitivity (BFU2011-26608) and the European Seventh Framework Program (612146/FP7-ICT-2013-10).

PLACNET review

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Leitao Huo

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