Step 2: Obtaining example dataset





Our sample dataset is ESTs for three different tomato genotypes publicly available at NCBI web site. It was downloded by running three queries:

"txid4081"[Organism] AND EST[PROP] - to extract all ESTs for genotype Lycopersicon esculentum

"txid62890"[Organism] AND EST[PROP] - to extract all ESTs for genotype Lycopersicon hirsutum

"txid28526"[Organism] AND EST[PROP] - to extract all ESTs for genotype Lycopersicon pennellii

Note: this pipeline was designed by year 2003. Since that time a sligthly different approach and improved scripts were developed. You can check the current protocol of EST selection and SNP discovery here.