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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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

Download


Documentation


Maintainers


  • person_outline Ferndo de la Cruz <>
  • person_outline Luis Vielva <>

Publications for PLAsmid Constellation NETwork

PLACNET in publications

 (9)
PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18

[…] 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 […]

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

[…] 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 […]

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

[…] were sequenced. in silico determinations of serotypes, sts/psts and fimh alleles fully agreed with experimental data., in order to establish the plasmid content of the seven e. coli genomes, the placnet protocol was used for plasmid reconstruction (supplementary figure ). as shown in table , plasmids were found in all isolates in numbers ranging from one (ec-huca 5) to seven (ec-huca 4). […]

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 […]

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

[…] 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, […]


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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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