pATLAS


30395323	Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. [PMID: 30395323] Jesus TF, Ribeiro-Gonçalves B, Silva DN, Bortolaia V, Ramirez M, Carriço JA. Abstract 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. Nucleic Acids Res. 2019:47(D1) \| 20 Citations (from Europe PMC, 2025-03-22)

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. [PMID: 30395323]

Jesus TF, Ribeiro-Gonçalves B, Silva DN, Bortolaia V, Ramirez M, Carriço JA.

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.

Nucleic Acids Res. 2019:47(D1) | 20 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.patlas.site
Full name:	Plasmid ATLAS
Description:	a web-based tool enabling searching for a specific plasmid (or plasmids) of interest, visualize the available plasmid database and to identify plasmids contained in High Throughput Sequencing data.
Year founded:	2019
Last update:	2018-09-20
Version:	1.6.1
Accessibility:	Accessible
Country/Region:	Portugal

Data type:	DNA
Data object:	Animal Bacteria Fungi Plant
Database category:	Gene genome and annotation Raw bio-data
Major species:	NA
Keywords:	plasmid high-throughput

University/Institution:	University of Lisbon
Address:
City:
Province/State:
Country/Region:	Portugal
Contact name (PI/Team):	Tiago F Jesus
Contact email (PI/Helpdesk):	tiagofilipe12@gmail.com

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Database Commons a catalog of worldwide biological databases