SA-SSR

SA-SSR detects Simple Sequence Repeats (SSRs, microsatellites) in large DNA and RNA sequence datasets using suffix array–based algorithms.

Key Features:

• Suffix Array and LCP-Based Detection: Identifies SSRs using suffix arrays and longest common prefix (LCP) arrays for efficient and exhaustive repeat discovery.
• High-Sensitivity SSR Identification: Achieves complete SSR detection in benchmark evaluations and identifies additional SSRs compared to alternative tools.

Scientific Applications:

• Genetic Variability and Marker Analysis: Supports population genetics, phylogenetics, and forensic studies through comprehensive microsatellite detection in genomic and transcriptomic sequences.

Methodology:

SA-SSR constructs suffix arrays and corresponding longest common prefix arrays from input DNA or RNA sequences to systematically identify tandem repeat motifs and enumerate Simple Sequence Repeats with high computational efficiency.