Microsatellites, also referred to as simple sequence repeats (SSRs) or short tandem repeats (STRs) - are co-dominant molecular markers universally scattered within all organisms genomes. Microsatellites markers are highly popular due to their abundance, hyper-variability, multi-allelic, highly reproducibility and detection simplicity. Over past decades, they are extensively used in a variety of fundamental and applied biological sciences for prokaryotes, plants and animals studies. Microsatellites are also have extensively been exploited as genetic markers for diverse applications including genome mapping, genetic material characterization, population genetics and genome evolution studies.
Nowadays, with the development of genome sequencing technologies, hundreds of genome sequences have been decoded and released. This published genomes data and the availability of bioinformatics tools provides an important opportunity for scientists to identify simple sequence repeats that could be used to develop useful SSR markers. These markers can be used subsequently in different studies such as; variety identiﬁcation, genetic diversity evaluation, construction of genetic linkage maps, association mapping, and marker-assisted selection.
SSRome is a comprehensive, integrated database and pipelines for microsatellites mining, classification, comparative analysis and markers development across all organisms.
SSRome is a user-friendly, integrated, comprehensive and dynamic database and pipelines for exploring microsatellites in a wide range of organisms. In SSRome database, 40,296,920 microsatellite DNA motifs were identified across Plants, Metazoa, Prokaryotes, Mitochondrial and Chloroplast sequenced genomes, in addition to all available NCBI ESTs till March 2017, represent collectively 5492 living organisms. This huge number of identified SSRs motifs were detected based on analysis of 76,621,110,515 bases of DNA. Moreover, a total of 13,987,159.00 SSR primer pairs were designed, using Primer3 software. All stored datasets of microsatellites motifs and markers of 5492 living organisms can be downloaded freely in very convenient way. SSRome database will be updated constantly. In SSRome database, 3 main functional modules\pages were developed to cover all content of identified SSR motifs among analyzed 5492 living organisms including 'Database Search', 'Downloads' and 'Statistics'.
In addition to the SSRome database, SSRome provides three user-friendly pipelines, can help scientists\users to identify, classify and compare microsatellite motifs in both genomic and transcriptomic Genome-wide levels. This SSRome pipeline part also comes into 3 main functional modules\pages were developed to cover different types of SSRs mining analysis at Genome-wide level; including SSRome Genomic Pipeline', ' SSRome Transcriptomic Pipeline' and ' SSRome Comparative Analysis Pipeline'.
SSRome Genomic Pipeline (SGP)
SSRome Genomic Pipeline (SGP) is a user-friendly tool can help scientists to identify and localize microsatellites at the Genome-wide level. The SGP tool can classify generated results into ‘SSR repeats unique to genic regions’, ‘SSR repeats unique to intergenic regions’ and ‘SSR repeats overlapped between genic and intergenic regions’. In addition, SSRome Genomic Pipeline includes adjustable SSR repeat unit and primer design parameters and user selectivity to design SSR primers in genic regions only, or in intergenic regions only or in both across the whole genomic regions.
SSRome Transcriptomic Pipeline (STP) is a user-friendly tool can identify and localize microsatellites at whole Transcriptomic-wide level (RNA-Seq data) or short cDNA sequences. The STP pipeline can perform SSRs mining at both assembled RNA Sequences with or without annotation information. In the case of providing STP with RNA Sequences without annotation information, STP will BLAST the RNA-sequences against local NCBI database to elucidate their best matching. In addition, SSRome Transcriptomic Pipeline includes adjustable SSR repeat unit and primer design parameters.
SSRome Comparative Analysis Pipeline (SCAP)
SSRome Comparative Analysis Pipeline (SCAP) is a user-friendly pipeline can compare identified SSR motifs of any organism as generated using SSRome pipelines or any other SSR detection tools against the SSRome database. The SCAP pipeline will deliver comparing results in form of unique SSR motifs of submitted sequence (if found) and full comparative profile of this sequence in relevant of other organisms available in SSRome database.