SSREnricher

SSREnricher identifies and enriches polymorphic microsatellites (SSRs) from transcriptome sequences via comparative transcriptome analysis to develop polymorphic genetic markers.

Key Features:

• Automated Polymorphic SSR Enrichment: Automates enrichment of polymorphic SSRs within transcriptome datasets to increase the yield of polymorphic markers.
• Core Analysis Procedures: Implements six core procedures: SSR Mining; Sequence Clustering; Sequence Modification; Enrichment of Polymorphic SSRs; False-Positive Removal; and Results Output and Multiple Sequence Alignment.
• High Efficiency and Accuracy: Validation experiments confirmed that over 90% of SSRs identified as polymorphic by SSREnricher were experimentally validated.
• Increased Polymorphism Frequency: Produces a significantly higher frequency of polymorphic SSRs compared with traditional and high-throughput sequencing (HTS) methods (P < 0.05).

Scientific Applications:

• Genetic Diversity Studies: Facilitates assessment of genetic variation within and between populations using polymorphic SSR markers.
• Marker-Assisted Selection (MAS): Supplies polymorphic SSR markers to support marker-assisted selection in plant and animal breeding programs.
• Conservation Genetics: Enables genetic monitoring and management in conservation genetics via polymorphic SSR markers.

Methodology:

Processes transcriptome FASTA files (e.g., from Trinity) through SSR mining, sequence clustering, sequence modification, enrichment of polymorphic SSRs, false-positive removal, and multiple sequence alignment to identify and validate polymorphic SSRs.