SSRMMD

SSRMMD mines simple sequence repeats (SSRs, microsatellites) from assembled genomic and transcriptomic sequences to identify perfect and polymorphic SSR loci for marker development in population genetics, linkage mapping, and evolutionary studies.

Key Features:

• Enhanced regular expressions: Uses enhanced regular expressions to exhaustively identify perfect SSR loci within assembled sequences of any size.
• Three-stage polymorphic SSR method: Implements a three-stage method specifically aimed at mining polymorphic SSRs.
• Flanking sequence conservativeness assessment: Assesses the conservativeness of SSR flanking sequences as part of polymorphic marker identification.
• Sliding window fragmentation: Applies a sliding window technique to fragment each assembled sequence for downstream evaluation.
• Fragment uniqueness evaluation: Evaluates the uniqueness of sequence fragments to identify candidate polymorphic SSR markers.
• Exhaustive perfect SSR mining: Exhaustively identifies perfect SSR loci across input assemblies.
• Rapid computational speed: Designed for rapid processing of large assemblies.
• Independence from other software: Operates independently of other external software tools.
• Portability: Implemented to support use across computational environments.
• Perl implementation: Implemented in Perl.
• Experimental validation: Polymorphic SSRs identified by the method have been validated by molecular biology assays.

Scientific Applications:

• Population genetics: Generates SSR markers for population genetic analyses and diversity studies.
• Linkage mapping: Provides polymorphic SSR markers for linkage map construction.
• Evolutionary biology: Supports investigation of genetic variation and evolutionary relationships.
• Marker development: Produces candidate polymorphic SSR markers for genetic and breeding applications.
• Genome and transcriptome mining: Mines SSRs from assembled genomes and transcriptomes across diverse organisms.

Methodology:

Uses enhanced regular expressions to identify perfect SSR loci and a three-stage polymorphic SSR mining method that assesses flanking sequence conservativeness, fragments assembled sequences with a sliding window, and evaluates fragment uniqueness; implemented in Perl.