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Plasmid ATLAS:plasmid visualanalytics andidentification inhigh-throughputsequencing data Tiago F. JesusBruno Ribeiro-GonçalvesDiogo Nuno Silva2018 год

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data
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Аннотация: Plasmid ATLAS (pATLAS, http://www.patlas.site) provides an easy-to-use web accessible database with visual analytics tools to explore the relationships of plasmids available in NCBI's RefSeq database. pATLAS has two main goals: (i) to provide an easy way to search for plasmids deposited in NCBI RefSeq and their associated metadata; (ii) to visualize the relationships of plasmids in a graph, allowing the exploration of plasmid evolution. pATLAS allows searching by plasmid name, bacterial host taxa, antibiotic resistance and virulence genes, plasmid families, and by sequence length and similarity. pATLAS is also able to represent in the plasmid network, plasmid sets identified by external pipelines using mapping, mash screen or assembly from high-throughput sequencing data. By representing the identified hits within the network of relationships between plasmids, allowing the possibility of removing redundant results, and by taking advantage of the browsing capabilities of pATLAS, users can more easily interpret the pipelines' results. All these analyses can be saved to a JSON file for sharing and future re-evaluation. Furthermore, by offering a REST-API, the pATLAS database and network display are easily accessible by other interfaces or pipelines.
Год издания: 2018
Авторы: Tiago F. Jesus, Bruno Ribeiro-Gonçalves, Diogo Nuno Silva, Valeria Bortolaia, Mário Ramirez, João André Carriço
Издательство: Oxford University Press
Источник: Nucleic Acids Research
Ключевые слова: Genomics and Phylogenetic Studies, Bacterial Identification and Susceptibility Testing, Identification and Quantification in Food
Другие ссылки: Nucleic Acids Research (PDF)
Nucleic Acids Research (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (PDF)
Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (HTML)
Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (HTML)
PubMed Central (HTML)
PubMed (HTML)