MISA

MISA identifies and localizes simple sequence repeats (SSRs), including perfect and compound microsatellites interrupted by a defined number of bases, within nucleotide sequences to support SSR marker development, genetic mapping, and diversity analysis.

Key Features:

• Identification of SSRs: Detects dimeric, trimeric, tetrameric and higher-order repeat motifs and localizes perfect microsatellites within nucleotide sequences.
• Compound SSR detection: Identifies compound microsatellites that are interrupted by a defined number of bases.
• EST database analysis: Has been applied to large-scale expressed sequence tag (EST) datasets, for example barley ESTs comprising 24,595 sequences.
• Marker development support: Facilitates identification of polymorphic SSR loci among cultivars or populations and supports designing primer pairs flanking SSR loci.

Scientific Applications:

• Genetic Mapping: Integration of EST-derived SSR markers into a barley genetic consensus map for linkage analysis.
• Polymorphism Analysis: Assessment of polymorphism levels among SSRs with observed correlations between repeat number and polymorphic variation.
• Cross-Species Transferability: Development of SSR markers transferable to related species such as rye, wheat, rice, and Hordeum bulbosum.
• cDNA-SSR Development: Exploitation of EST databases for development of cDNA-based microsatellite markers.
• Comparative Genomics: Generation of SSR-based diversity patterns comparable to those obtained from RFLP markers for cross-species comparisons.

Methodology:

Scans nucleotide sequences to identify repeat motifs and localize perfect and compound SSRs; aids in designing primer pairs flanking SSR loci; analyzes EST-derived SSRs for polymorphism and diversity assessment.