CRISPRcompar

CRISPRcompar performs comparative and evolutionary analysis of CRISPR loci, using direct repeats (DRs) and spacer sequences to type bacterial strains and infer their relationships.

Key Features:

• CRISPR locus analysis: Analyzes CRISPR loci composed of direct repeats (DRs) and spacers for comparative and evolutionary study.
• Direct repeat characteristics: Recognizes conserved DRs ranging from 24 to 47 base pairs.
• Spacer sequence diversity: Captures unique spacer sequences and their variability for strain differentiation.
• Polar acquisition: Accounts for the acquisition of new repeat+spacer units predominantly on one side of the locus.
• CRISPR typing support: Facilitates CRISPR typing to discriminate closely related bacterial strains and infer relationships.
• Module — CRISPRcomparison: Enables in silico comparative analysis of CRISPR loci across bacterial strains.
• Module — CRISPRtionary: Enables in silico investigations to assist CRISPR typing.

Scientific Applications:

• Strain discrimination: Differentiates closely related bacterial strains using spacer variability and DR conservation.
• Comparative genomics: Compares CRISPR loci across strains to inform comparative genomics studies.
• Microbial evolution and diversity: Infers evolutionary relationships and diversity patterns among prokaryotes (archaea and bacteria) using CRISPR variation.
• Phage resistance studies: Relates spacer content to acquired resistance against phages.

Methodology:

Performs in silico comparative analysis via the CRISPRcomparison and CRISPRtionary modules focusing on direct repeats and spacer sequences.