ESAP plus

ESAP plus processes Expressed Sequence Tags (ESTs) to identify EST-derived Simple Sequence Repeat (SSR) loci and design SSR primers for marker development from mRNA-derived cDNA in plants.

Key Features:

• Comprehensive Workflow: Implements four procedures for EST-SSR development: pre-processing, clustering and assembly, SSR mining, and SSR primer design.
• Pre-processing: Performs initial handling and filtering of raw EST sequences prior to downstream analysis.
• Clustering and Assembly: Groups similar ESTs to reduce redundancy and assemble contigs for accurate SSR detection.
• SSR Mining: Identifies Simple Sequence Repeat loci within assembled EST sequences.
• SSR Primer Design: Generates primers for PCR amplification of identified SSR regions.
• Alternative Steps: Provides optional procedures to further minimize EST redundancy and enhance SSR locus identification.
• Database Integration: Stores input EST data and predicted SSR results in a MySQL database.
• Scalability: Capable of processing large EST datasets for extensive marker development projects.

Scientific Applications:

• EST-SSR marker development: Enables discovery and primer design for EST-derived SSR markers from mRNA/cDNA sequences.
• Genetic mapping: Supplies SSR markers suitable for linkage map construction in plants.
• Population structure and diversity analysis: Provides markers for assessing allelic variation and population genetics.
• Marker-assisted selection: Produces SSR markers applicable to breeding programs.
• Research in species without reference genomes: Facilitates marker development for plants lacking whole-genome sequences.

Methodology:

Computational steps explicitly include EST pre-processing, clustering and assembly to form contigs, SSR mining to detect repeat loci, SSR primer design for identified loci, and storage of EST and SSR results in a MySQL database.