Micro-Primers

Micro-Primers automates screening of microsatellites (SSRs) and the design of PCR primers for multi-individual genomic libraries to enable population-level characterization of genetic diversity.

Key Features:

• NGS data processing: Processes fastq files generated by next-generation sequencing (NGS) and integrates commonly used programs for data cleaning and microsatellite mining.
• Microsatellite (SSR) screening: Identifies and characterizes SSR loci across sequences from multiple individuals.
• Primer design: Designs PCR primers for amplification of identified SSR loci and reports PCR product sizes.
• Population-level metrics: Reports allele counts within population subsets and melting temperatures for primer sets.
• Polymorphic locus identification: Identifies potential polymorphic loci based on observed allele ranges within the population.
• Performance: Demonstrates reduced processing time compared to manual methods, with duration depending on sequence number.
• Bottleneck mitigation: Automates selection of polymorphic loci from multiple individuals to address a common bottleneck in population studies.
• Implementation: Implemented in Python.

Scientific Applications:

• Conservation genetics: Inform management decisions by assessing genetic diversity and identifying markers relevant to species conservation.
• Marker development: Develop species-specific microsatellite markers via primer design for SSR loci.
• Population genetics: Characterize intra- and inter-population genetic diversity and allele distribution patterns from multi-individual libraries.

Methodology:

Processes fastq NGS data with integrated data cleaning and microsatellite mining programs, characterizes SSRs at the population level, designs PCR primers for identified loci, and identifies polymorphic loci from observed allele ranges; implemented in Python.