CRISPRFinder

CRISPRFinder identifies CRISPR arrays in prokaryotic genomes and extracts their direct repeats, spacers, and flanking leader sequences to support analysis of prokaryotic adaptive immunity.

Key Features:

• Detection of CRISPRs: Identifies CRISPR clusters within genomic sequences, including arrays with as few as one or two repeats.
• Definition and Extraction of Direct Repeats (DR) and Spacers: Defines direct repeats (DR) ranging from 23 to 47 base pairs and extracts unique spacer sequences typically derived from viral origins.
• Flanking Sequence Analysis: Identifies the AT-rich leader sequence flanking the CRISPR cluster on one side, hypothesized to function as a transcriptional promoter.
• Database Comparison with BLAST: Performs BLAST searches of extracted spacers against the GenBank database to identify matching viral sequences.
• Cross-Genomic Analysis: Checks for the presence of identified direct repeats across other sequenced prokaryotic genomes to assess their distribution and conservation.

Scientific Applications:

• Microbial adaptive immunity: Enables characterization of CRISPR structures to study RNA-interference-based immune systems in bacteria and archaea.
• Host–pathogen interactions and viral provenance: Links spacer sequences to known viral genomes via BLAST to infer past viral exposures and dynamics of host–pathogen relationships.

Methodology:

Uses algorithms to detect CRISPR arrays, define direct repeats and spacers, identify AT-rich leader sequences, perform BLAST comparisons against GenBank, and survey direct repeat occurrences across sequenced prokaryotic genomes.