FullSSR: Microsatellite Finder and Primer Designer

CABRERA, JUAN MANUEL; AMAVET, PATRICIA SUSANA; RUEDA, EVA CAROLINA; METZ, SEBASTIÁN; GIRI, FEDERICO; CABRERA, JUAN MANUEL; RUEDA, EVA CAROLINA; AMAVET, PATRICIA SUSANA; METZ, SEBASTIÁN; GIRI, FEDERICO

Advances in Bioinformatics

Hindawi

Lugar: El Cairo; Año: 2016 vol. 2016

1687-8027

Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markersin population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design usinggenomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from theNational Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454 from Caimanlatirostris, Salvator merianae,Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similarSSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, resultscan be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs andprimer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis toolspipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.