oriTfinder

oriTfinder identifies origin of transfer (oriT) sites in conjugative plasmids and chromosome-borne integrative and conjugative elements to enable annotation of transfer-related modules and assessment of potential dissemination of antibiotic resistance and virulence determinants.

Key Features:

• oriTDB: A curated database containing over one thousand archived oriT nucleotide sequences.
• Similarity search: Performs similarity searches against archived oriT nucleotide sequences from oriTDB.
• Co-localization analysis: Performs co-localization analysis to identify flanking genes homologous to known relaxase genes.
• Transfer module detection: Detects potential relaxase genes, type IV coupling protein (T4CP) genes, and type IV secretion system (T4SS) gene clusters.
• oriT localization: Identifies oriT sites within conjugative plasmids and chromosome-borne integrative and conjugative elements (ICEs).
• Association with resistance and virulence: Identifies putative genes linked to virulence factors and antibiotic resistance determinants co-localized with oriT.

Scientific Applications:

• Re-annotation of mobile elements: Supports re-annotation of bacterial conjugative, mobilizable, or non-transferable elements.
• Risk assessment of gene dissemination: Enables assessment of the potential dissemination of antibiotic resistance and virulence factors in pathogenic bacteria.
• Support for mitigation strategies: Supports efforts to understand and mitigate the spread of antibiotic resistance and virulence factors.

Methodology:

Performs similarity searches against oriTDB (over 1,000 oriT nucleotide sequences) and co-localization analysis to identify flanking genes homologous to known relaxases, and detects relaxase genes, T4CP genes, T4SS gene clusters, and putative virulence and antibiotic resistance genes.