MegaSSR

MegaSSR identifies, classifies, and designs SSR (Simple Sequence Repeat) markers from next-generation sequencing genomic data to support molecular diversity studies and breeding programs.

Key Features:

• SSR Marker Design: Designs targeted PCR-based primers for selected SSR repeats to enable marker development.
• SSR Mining and Classification: Performs large-scale identification and classification of microsatellites across genomic data.
• Comparisons and Statistical Visualization: Produces comparative analyses and statistical visualizations of SSR distributions and properties.
• In Silico PCR Validation: Validates designed primers through in silico PCR simulations.
• Pipeline Integration and Scalability: Automates SSR marker development by integrating multiple bioinformatics tools into a pipeline capable of handling large datasets.

Scientific Applications:

• Plant genetics and breeding: Supports SSR marker discovery and primer design for plant species research and breeding programs.
• Molecular diversity studies: Enables characterization of genetic diversity using SSR markers derived from NGS genomic data.
• Genetic resource characterization: Facilitates development of SSR markers for assessment and management of genetic resources.

Methodology:

Utilizes next-generation sequencing genomic data to identify and classify microsatellites and automates SSR marker development by integrating multiple bioinformatics tools into a pipeline that performs in silico PCR validation and handles large datasets.