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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 Pipemicrodb (Pigeonpea Microsatellite database), a web based relational database of microsatellites present in the whole genome sequence. Pipemicrodb 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.

PipeMicrodb is available at http://cabindb.iasri.res.in/pigeonpea/

 

Citation:
Sarika, Vasu Arora, M. A. Iquebal, Anil Rai, and Dinesh Kumar. PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome. Database (2013) Vol. 2013: article ID bas054; doi:10.1093/database/bas054. Impact Factor 3.179