On each side of the SSR there are flanking regions that are critical to develop locus-specific primers to amplify the microsatellites by PCR. An alternative method is using Next Generation Sequencing (NGS) to obtain a great number of sequences reducing the costs at the same time. Traditional methods to isolate SSRs included the construction of enriched genomic libraries, cloning, and sequencing however this approach is time-consuming and very expensive. SSRs have been widely used as molecular markers in population biology because they have high mutation rates with high levels of polymorphism between organisms of the same population. Microsatellites (also known as “Short Sequence Repeats” (SSRs)) are genomic sequences comprised of tandem repeats of short nucleotide motifs (1 to 6 bp). The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. FullSSR simplifies the detection of SSRs and primer design on a big data set. In addition, results can be affected by the analyzed sequences because of differences among the genomes. The results of the use of this kind of approach depend on the parameters set by the user.
FullSSR performance was compared against other similar SSR search programs.
The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics.