Tandem repeats (TRs) are consecutive sequence duplicates abundant in both coding and noncoding genomic sequences. Short TRs of DNA, known as microsatellites, have been discovered by accident in human samples, and since have been used successfully as markers in forensics and for genetic profiling. Although most TRs are found in noncoding sequences, mounting evidence suggests their substantial presence in protein coding genes: at least in 14% of proteins in all kingdoms of life, and of much higher frequency in eukaryotes.
A comprehensive online database of all SSRs (Simple Sequence Repeats) or STRs (Short Tandem Repeats) or Microsatellites from all sequenced Chloroplast and Mitochondrial genomes available so far across all the clades of life. SSRs are considered as important genomic elements and play a major role in the understanding the underpinnings of the evolution, linkage analysis and species discrimination. ChloroMitoSSRDB 2.0 provides a wide accessible platform for accessing the microsatellites patterns using the IMEx (Imperfect Microsatellite Extractor) and MISA and along with the primer pair information for the same. Additionally, the present version of the web-servers also allows the users to analyze the whole genome, genes and also NGS reads for the identification of the SSRs.
Provides information of all the three types (perfect, imperfect and compound) of simple sequence repeats (SSRs). In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. ChloroSSRdb is a relational database developed using SQL server 2008 and accessed through ASP.NET.
Provides information about perfect, imperfect and compound Simple Sequence Repeats (SSRs). MitoSatPlant is an online resource of plant mitochondrial SSRs (mtSSRs). Additionally, Polymerase Chain Reaction (PCR) primers, statistical information such as density, average length of SSRs, frequencies of repeat type are also available. User can freely download the data available in this database which will help researchers to screen polymorphic markers in plant mitochondrial DNA.
It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their microsatellite allele size(s), it provides users additional morphological and chemical information for each identified cultivar. Currently, OGDD is designed to enable users to easily retrieve and visualize biologically important information (SSR markers, and olive tree and oil characteristics of about 200 cultivars worldwide) using a set of efficient query interfaces and analysis tools. Compared with other few existing databases for olive species, OGDD has its own specific features and advantages. In fact, it provides a reference system in evaluating the data obtained from the analysis of unknown samples and in defining the varietal composition of the virgin olive oil. It also contains a great deal of information for each cultivar identified by the user. This database can be used by all researchers and stakeholders interested in olive cultivar identification and virgin olive oil authentication.
Provides a platform to study the associations between disease genes and previously uncharacterized tandem repeats which is a key to understanding the mechanisms of pathogenicity of such diseases. These associations, together with the data indicating distribution patterns in protein-coding and non-coding regions can help direct future research into identifying the evolutionary history and functional significance of tandem repeats. In contrast to other available databases, TRbase identifies both perfect and imperfect repeats of 1-2000 bp unit lengths.
A database to study microsatellite DNAs and marker development in a wide range of plant species and genome evolution. InPMDBase, 26,230,099 microsatellite DNA entries were identified among 110 genome sequenced plant species. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and customized software.
Provides a database containing information for specimens collected throughout the native range in North America, Greenland and Russia. Boechera Microsatellite Website includes a variety of search algorithms that aims to assign the correct taxon name, ploidy, reproductive mode, and hybrid parentage to any Boechera specimen with appropriate microsatellite data.