PLSDB

PLSDB provides a curated database of bacterial plasmid sequences for sequence comparison and analysis to support investigation of plasmid-borne antibiotic resistance and virulence genes in metagenomic and isolate sequencing studies.

Key Features:

• Curated annotated plasmid collection: A curated collection of annotated bacterial plasmid sequences for reference-based sequence comparison.
• Sequence comparison and similarity information: Enables comparison of custom sequences against the database and reporting of similarity information to reference plasmids.
• Data quality filtering and annotations: Applies filtering steps and additional annotations to refine records and reduce false positives from misassemblies.
• API and Python library: Provides programmatic access for remote database queries and integration into automated bioinformatics workflows.

Scientific Applications:

• Plasmid identification and characterization: Identification and characterization of plasmids carrying antibiotic resistance genes and virulence factors in metagenomic and isolate sequencing datasets.
• Assessment of assembly and false positives: Detection and reduction of false-positive plasmid calls arising from misassemblies through reference comparison and filtering.
• Integration into automated analyses: Integration into large-scale screening and comparative plasmid analyses via API and Python library for automated pipelines.

Methodology:

Uses a curated collection of annotated plasmid sequences with implemented filtering steps and annotations, supports sequence comparison against the database, and offers programmatic access via an API and a Python library.