Molecular markers play a significant role for crop improvement in desirable characteristics, such as resistance to disease, high growth rate and other characteristics that will benefit the plant and variety in long term.
Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed BrassicaSatDb (Brassica Microsatellite Database ), a web based relational database of microsatellites present in the whole genome sequence. BrassicaSatdb allows microsatellite search using multiple parameters like microsatellite type simple and compound, repeat type (mono- to hexa-nucleotide), copy number, microsatellite length, pattern of the repeat motif itself and the location of the marker on the chromosome. Microsatellites can be retrieved by specifying the chromosome number (or numbers). The database also searches the specified number of markers in a provided location range on a particular chromosome. The nucleotide sequences of the particular marker are also provided to facilitate primer designing for PCR amplification of any desired microsatellite.
BrassicaSatdb is available at http://cabindb.iasri.res.in/brassica/
BrassicaSatDb also fulfils this customized search according to the requirement of researcher, on ranges of GC content, base pair and copy number. This database has been further appended with Primer3 for primer designing of the selected markers with left and right flankings of size upto 500 base pairs, which will enable researcher to select markers of choice at desired interval over the chromosome. A novel add-on for degenerate bases has been incorporated in this database search, where the users are given flexibility to replace degenerate bases with any of the alternative base (A,T,G,C). This feature has been added to resolve the issue of some of the degenerate bases present in current genome assembly making the primer designing very difficult otherwise.
