WASPS

WASPS performs comparative analysis of plasmid genomes by generating synteny maps and supporting protein and DNA sequence similarity searches against a database of completely sequenced natural plasmids.

Key Features:

• Comprehensive Database: Includes all completely sequenced natural plasmids from bacterial, archaeal, and eukaryotic origins.
• Sequence Similarity Searches: Supports protein and DNA sequence similarity searches against the plasmid database.
• Orthologous Protein Clustering: Pre-calculates orthologous protein clusters within the database to inform synteny analyses.
• Real-Time Synteny Map Generation: Generates fully resolved plasmid synteny maps in real time and accepts internal or custom DNA sequences as input.

Scientific Applications:

• Comparative Genomics: Enables detailed synteny analysis across diverse plasmid datasets to identify conserved genetic elements.
• Evolutionary Biology: Supports identification of orthologous relationships and analysis of plasmid evolution and horizontal gene transfer events.
• Microbial Ecology: Facilitates exploration of plasmid-mediated functions, including antibiotic resistance dissemination, across microbial communities.

Methodology:

Maintains a database of all completely sequenced natural plasmids from bacteria, archaea, and eukarya; performs protein and DNA sequence similarity searches; uses pre-calculated orthologous protein clusters to generate synteny maps in real time and accepts internal or custom DNA sequences as input.