Molecular marker is a polypeptide or piece of DNA with easily identified phenotype such that cells or individuals with different alleles are distinguishable. A microsatellite or Simple Sequence Repeat (SSR) is a section of DNA in which certain DNA motifs (ranging in length from 1-5 base pairs) are tandemly repeated, typically 5-50 times. Microsatellites occur at thousands of locations within an organism's genome having a higher mutation rate than other areas of DNA leading to high genetic diversity. Polymorphism is the sequence differences where individual variations arise at an average rate of one nucleotide base difference per 1000 bases. When the mutant allele of a gene exceeds 1% representations in a population, we can call it as polymorphism.

This polymorphism detection tool, PolyMorphPredict has three modules which work together irrespective of the languages used like Perl (64 bit, version 5), R (version 3.0) or Java (version 7). Such type of tool is required for agriculture research as DNA marker based breeding does not have transgenic issues. It will help in better identification of genes, QTL controlling trait, increase in marker density and localisation of scaffolds over linkage map. It will give better precision than QTL mapping, physical absolute distance rather than relative distance mapping. SSR polymorphism tool can be applied in crop sciences for diversity and core set analysis, QTL mapping, association mapping, MAS, DUS testing. It also has wide application in animal sciences for diversity analysis, breed identification, mapping, kinship and parentage identification as well as traceability of product.