GMATo: A novel tool for the identification and analysis of microsatellites in large genomes

Abstract

Simple Sequence Repeats (SSR), also called microsatellite, is very useful for genetic marker development and genome applicati\ron. \rThe increasing whole sequences of more and more large genomes provide sources for SSR mining \rin silico\r. However currently \rexist\ring SSR mining tools can’t process large genomes efficiently and generate no or poor statistics. Genome\r-\rwide Microsatellite \rAnalyzing Tool (GMATo) is a novel tool for SSR mining and statistics at genome aspects. It is faster and more accurate than e\rxisted \rtools SSR Locator and MISA. If a DNA sequence was too long, it was chunked to short segments at several Mb followed by motifs\rgeneration and searching using Perl powerful pattern match function. Matched loci data from each chunk were then merged to \rproduce\rfinal SSR loci information. Only one input file is required which contains raw fasta DNA sequences and output files in \rtabular format list all SSR loci information and statistical distribution at four classifications. GMATo was programmed in Ja\rva and \rPerl\rwith both graphic and command line interface, either executable alone in platform independent manner with full parameters \rcontrol. Software GMATo is a powerful tool for complete SSR characterization in genomes at any size