msatcommander

msatcommander detects microsatellite (SSR, VNTR) repeats in DNA sequences and designs locus-specific and tag primers to support PCR-based genetic analyses.

Key Features:

• Microsatellite Array Detection: Locates microsatellite (SSR, VNTR) repeats in DNA sequences for downstream marker analysis.
• Primer Design: Automates design of locus-specific primers for PCR amplification of identified microsatellites.
• Tag Primer Generation: Generates tag primers to increase specificity for downstream genetic assays.
• Data Output: Exports search results and primer information in comma-separated value (CSV) format.

Scientific Applications:

• Genetic mapping: Provides microsatellite loci and primers for constructing linkage maps.
• Biodiversity assessment: Enables detection of polymorphic SSR loci for species and population diversity analyses.
• Conservation genetics: Supplies markers and primers for assessing genetic variation in threatened or managed populations.
• Evolutionary studies: Identifies microsatellite variation used in population structure and evolutionary inference.
• Population genetics: Detects SSR variation applicable to allele frequency, heterozygosity, and related analyses.

Methodology:

Searches DNA sequences for microsatellite (SSR, VNTR) repeats, designs locus-specific and tag primers for PCR amplification, and exports results in CSV format.