cblaster

cblaster identifies clusters of co-located homologous sequences in local and remote sequence databases to detect gene clusters involved in coordinated biological pathways such as metabolism, drug resistance, and virulence.

Key Features:

• Remote and Local Database Searches: Uses the NCBI BLAST API for remote searches and DIAMOND for local database queries.
• Detection of Co-located Homologous Gene Clusters: Identifies groups of homologous sequences that are co-located on genomes to define candidate gene clusters.
• User-Defined Filtering Criteria: Supports thresholds for identity, coverage, and e-value to filter search results.
• Integration with NCBI IPG and Local Databases: Retrieves genomic coordinates from the NCBI Identical Protein Group (IPG) database for remote hits and uses user-provided databases to obtain coordinates for local searches.
• BLAST Result Parsing and Filtering: Parses and filters BLAST search results according to user-defined criteria to extract relevant hits.
• Visualization Outputs: Generates outputs suitable for visualization of large datasets and gene cluster arrangements.

Scientific Applications:

• Comparative Genomics: Identifying homologous gene clusters across species and strains to compare cluster presence, composition, and conservation.
• Functional Analysis of Pathways: Detecting gene clusters involved in coordinated biological pathways such as metabolism, drug resistance, and virulence.
• Evolutionary Studies: Investigating the evolution and distribution of gene clusters to infer evolutionary relationships.

Methodology:

Implements remote searches via the NCBI BLAST API and local searches via DIAMOND, retrieves genomic coordinates from the NCBI Identical Protein Group (IPG) database or user-provided databases, parses and filters BLAST search results using identity, coverage, and e-value thresholds, and is implemented in Python.