PLSDB: advancing a comprehensive database of bacterial plasmids
| Autor: | Fabian Kern, Anna Hartung, Rolf Müller, Tobias Fehlmann, Georges Pierre Schmartz, Andreas Keller, Pascal Hirsch |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
Firmicutes Biology computer.software_genre User-Computer Interface Upload Databases Genetic Proteobacteria Genetics False positive paradox Database Issue Preprocessor Relevance (information retrieval) computer.programming_language Internet Bacteria Virulence Database Application programming interface Bacteroidetes Drug Resistance Microbial Molecular Sequence Annotation Python (programming language) Actinobacteria Workflow Metagenomics Spirochaetales computer Tenericutes Plasmids |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkab1111 |
| Popis: | Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb. Graphical Abstract Graphical AbstractPLSDB aggregates plasmid and meta data from different public resources. This data passes through several enhanced annotation and filtering steps. Finally, the information is presented in a web-server, providing two new functionalities. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|