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María de Toro

dblp:210/9275 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2017
0000-0003-3329-0203ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis › sequence assembly
genome assembly
0.312017
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes · Bioinform. 2017
Bioinformatics and computational biology › sequence analysis › sequence assembly
plasmid reconstruction
0.312017
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes · Bioinform. 2017
Bioinformatics and computational biology › sequence analysis › sequence assembly
scaffold graph analysis
0.312017
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes · Bioinform. 2017

Methods — techniques the papers use, named apart from their topics

graph pruning · 0.3BLAST · 0.3
YearPublicationVenuePosition
2017 PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes
abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: PLACNETw is freely available at https://castillo.dicom.unican.es/upload/. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: A tutorial video and several solved examples are available at https://castillo.dicom.unican.es/placnetw_video/ and https://castillo.dicom.unican.es/examples/.
Luis Vielva, María de Toro, Val F. Lanza, Fernando de la Cruz
Bioinform.2