CrisprVi

CrisprVi visualizes and analyzes clustered regularly interspaced short palindromic repeats (CRISPR) sequences to provide detailed insights into CRISPR-Cas loci across multiple prokaryotic genomes.

Key Features:

• DR and spacer labeling and alignment: Labels and aligns CRISPR direct repeats (DRs) and spacers to represent their genomic locations, orders, and components.
• Data processing and storage: Performs command parsing and data transmission and stores processed data in local SQLite databases and BLAST databases for sequence alignment and comparison.
• Statistical analysis: Computes basic statistics on CRISPR sequences to quantify sequence variability and distribution.
• Consensus inspection via clustering: Inspects consensus sequences of DRs and spacers and generates clustering heatmaps derived from BLAST results to assess similarity across strains.
• Comparative genome analysis: Enables analysis of CRISPR loci across multiple genomes to support identification and characterization of CRISPR-Cas systems.

Scientific Applications:

• Identification and characterization: Identification and characterization of novel CRISPR loci and their components across strains or species.
• Comparative genomics: Comparative analysis of CRISPR sequences from multiple prokaryotic genomes to investigate evolutionary relationships and functional diversification of CRISPR-Cas systems.
• Consensus and variability analysis: Analysis of consensus sequences, sequence variability, and distribution of DRs and spacers using statistical measures and BLAST-derived clustering.

Methodology:

Implemented as a Python package that performs command parsing and data transmission, stores data in local SQLite and BLAST databases, aligns and labels DRs and spacers, computes basic statistics, and produces BLAST-derived clustering heatmaps.