{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T09:47:39Z","timestamp":1769939259567,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2017,7,21]],"date-time":"2017-07-21T00:00:00Z","timestamp":1500595200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background. PLACNETw, a webtool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making. It allows a user with domain expertise to visualize the scaffold graphs and related information of contigs as well as reference sequences, so that the pruning operations can be done interactively from a personal computer without the need for additional tools. After successful pruning, each plasmid becomes a separate connected component subgraph. The resulting data are automatically downloaded by the user.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PLACNETw is freely available at https:\/\/castillo.dicom.unican.es\/upload\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>A tutorial video and several solved examples are available at https:\/\/castillo.dicom.unican.es\/placnetw_video\/ and https:\/\/castillo.dicom.unican.es\/examples\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx462","type":"journal-article","created":{"date-parts":[[2017,7,20]],"date-time":"2017-07-20T08:10:32Z","timestamp":1500538232000},"page":"3796-3798","source":"Crossref","is-referenced-by-count":119,"title":["PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes"],"prefix":"10.1093","volume":"33","author":[{"given":"Luis","family":"Vielva","sequence":"first","affiliation":[{"name":"Departamento de Ingenier\u00eda de Comunicaciones, Universidad de Cantabria, Santander, Spain"}]},{"given":"Mar\u00eda","family":"de Toro","sequence":"additional","affiliation":[{"name":"Plataforma de Gen\u00f3mica y Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica de La Rioja (CIBIR), Logro\u00f1o, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0870-9500","authenticated-orcid":false,"given":"Val F","family":"Lanza","sequence":"additional","affiliation":[{"name":"Departamento de Microbiolog\u00eda, Instituto de Investigaci\u00f3n Sanitaria Ram\u00f3n y Cajal (IRYCIS), Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3329-0203","authenticated-orcid":false,"given":"Fernando","family":"de la Cruz","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnolog\u00eda de Cantabria (Universidad de Cantabria\u2013CSIC), Santander, Spain"}]}],"member":"286","published-online":{"date-parts":[[2017,7,21]]},"reference":[{"key":"2023020207005993900_btx462-B1","author":"Antipov","year":"2016"},{"key":"2023020207005993900_btx462-B2","article-title":"On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data","author":"Arredondo-Alonso","year":"2017","journal-title":"bioRxiv"},{"key":"2023020207005993900_btx462-B3","doi-asserted-by":"crossref","first-page":"e1004776","DOI":"10.1371\/journal.pgen.1004776","article-title":"Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages","volume":"10","author":"de Been","year":"2014","journal-title":"PLoS Genet"},{"key":"2023020207005993900_btx462-B4","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. 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