Krait

Krait detects perfect, imperfect, and compound microsatellites genome-wide and designs PCR primers via Primer3 to support microsatellite-based genetic and disease analyses.

Key Features:

• Comprehensive Microsatellite Identification: Identifies perfect, imperfect, and compound microsatellites across whole-genome sequences.
• Primer3 integration: Integrates with Primer3 to design primers for microsatellite amplification.
• Data export and reporting: Exports results in FASTA and GFF3 formats and generates statistical reports and visual plots.
• Implementation: Implemented in C and Python.

Scientific Applications:

• Population genetics: Identification and genotyping of microsatellite markers for analyses of genetic diversity and evolutionary relationships.
• Medical research: Investigation of microsatellite instability and other disease-associated repeat variations.
• Genotyping and marker development: Design and evaluation of PCR primers for microsatellite amplification and marker development.
• Genome-wide surveys: Characterization of microsatellite distribution across genomes.

Methodology:

Krait performs genome-wide detection of perfect, imperfect, and compound microsatellites, integrates with Primer3 for primer design, exports outputs to FASTA and GFF3, and produces statistical reports and visual plots; it is implemented in C and Python.