EasySSR

EasySSR identifies and compares microsatellites (SSRs/STRs) in FASTA and GenBank genomic sequences to enable large-scale SSR mining, including detection of perfect and imperfect repeats in coding and non-coding regions.

Key Features:

• Input formats: Accepts FASTA files and optional GenBank files for one or more genomes.
• Genome-scale comparison: Supports identification and comparison of SSRs across entire genomes, including draft and complete assemblies.
• SSR detection: Identifies perfect and imperfect microsatellites (SSRs/STRs) within coding and non-coding regions.
• SSR metrics and attributes: Reports frequencies, abundance, repeat motifs, flanking sequences, and repeat iterations for detected SSRs.
• Output formats: Generates PTT files, Excel tables, and interactive charts for downstream analysis.
• GenBank conversion: Converts GenBank files into PTT format.

Scientific Applications:

• Comparative Genomics: Facilitates comparison of SSR distributions and motif variation to investigate evolutionary relationships.
• Molecular Biology: Assists study of genetic variation and its implications for gene function and regulation via SSR analysis.
• Forensics: Supports analysis of polymorphic STR regions for DNA profiling.

Methodology:

Automates SSR identification and comparative reporting and converts GenBank files into PTT format.