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Título: | PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes |
Autor: | Vielva, Luis; Toro, María de CSIC ORCID CVN; Lanza, Val F. CSIC; Cruz, Fernando de la CSIC ORCID | Fecha de publicación: | 2017 | Editor: | Oxford University Press | Citación: | Bioinformatics 33(23): 3796-3798 (2017) | Resumen: | 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. | Descripción: | Supplementary information: A tutorial video and various solved examples are available at Bioinformatics online and at the PLACNETw main page. | Versión del editor: | https://doi.org/10.1093/bioinformatics/btx462 | URI: | http://hdl.handle.net/10261/189719 | DOI: | 10.1093/bioinformatics/btx462 | ISSN: | 1367-4803 | E-ISSN: | 1460-2059 |
Aparece en las colecciones: | (IBBTEC) Artículos |
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Fichero | Descripción | Tamaño | Formato | |
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PLACNETw.pdf | 622,67 kB | Adobe PDF | Visualizar/Abrir |
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