PSMD

PSMD catalogs microsatellites (simple sequence repeats, SSRs/STRs) of 1–6 base pairs across 18,408 organisms to support comparative genomics, molecular marker development, and gene-associated SSR analysis.

Key Features:

• Comprehensive dataset: Contains 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms.
• SSR annotation: Annotates tandem repeats of 1–6 bp motifs (SSRs/STRs).
• Export formats: Provides data export in GFF3 for gene annotation and CSV for statistical analysis.
• Occurrence analysis module: Offers a microsatellite analysis tool that evaluates SSR occurrence using user-defined parameters.
• Primer design integration: Integrates Primer3 to support primer design with customizable settings.
• Gene annotation linkage: Associates microsatellites with gene and regulatory region annotations.

Scientific Applications:

• Genetic diversity studies: Enables use of highly polymorphic SSRs as genetic markers for population and diversity analyses.
• Gene regulation analysis: Facilitates investigation of SSRs located in or near regulatory regions for potential regulatory roles.
• Molecular marker development: Supports design and validation of SSR markers and primers for experimental assays.
• Disease research: Provides SSR data relevant to studies of genetic diseases, including cancers.
• Comparative genomics and genome-wide analyses: Enables cross-species comparison of microsatellite distribution patterns at the genome-wide scale.
• Applied biological studies: Supplies SSR resources applicable to biological, medical, environmental, and agricultural research.

Methodology:

Compiles microsatellites from available genomic data across 18,408 organisms, annotates perfect and compound SSRs, provides GFF3 and CSV exports, includes an occurrence analysis module with user-defined parameters, and integrates Primer3 for primer design.