Wgssat

Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes and RNAs. The features of WGSSAT were demonstrated using Takifugurubripes data. This yielded a total of 139057 SSR, out of which 113703 SSR primer pairs were uniquely amplified in silico onto a Takifugurubripes (fugu) genome. Out of 1,13,703 mined SSRs, 81,463 were from coding region (including 4,286 exonic and 77,177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 1,05,641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.[1]

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