An SSR comparative genomics database and its applications

Simple sequence repeats (SSRs) play as important genetic markers in genome mapping projects and polymorphic research. In this study, we have designed a database which facilitates the searching and position verification of SSRs and provides comparative genomics information among various species. However, performing in silico analysis of biological data sometimes attempts to result in high false positive rates. In order to promote the specificity of discovered SSRs from the proposed system, we take advantage of evolutionarily conserved segments among sequences from various species. Users are able to choose specific species as targets to filter out SSRs which are not located in conserved regions. Screening processes narrow down candidate SSRs and improve the performance of specificity. In this database, there are eleven representative species collected for comparative genomics analysis. Taking the comparison between zebrafish and medaka fish as an example, 60,363 SSRs from zebrafish genorne are found in conserved regions in which 6.20% SSRs are located in protein-coding regions, 0.20% in 5'UTR, 0.87% in 3'UTR, 51.26% in intron, and 41.45% in intergenic region. Each SSR is precisely allocated and annotated in this database for further applications.