SilkSatDb

The SilkSatDb (Silkworm Microsatellite Database) is a relational database of microsatellites extracted from the available sequences of the silkmoth, Bombyx mori. The database has been rendered with a simple and robust web based search facility, developed using PHP. The SilkSatDb also stores information on primers developed and tested in the laboratory. User can retrieve information on the microsatellite, the protocols used, along with informative figures and polymorphism status of those microsatellites. In addition to this, the interface is coupled with Autoprimer, a primer-designing program, which can be used to design primers for the loci of interest.

The design of the database schema basically follows the "Three-level schema architecture" as shown in Fig.1. The database stores three kinds of data: the microsatellite repeats found in B. mori EST and WGS sequences, sequence details and the primers developed for these microsatellites. Currently, the database encompasses information pertaining to 12,000 WGS, 9300 ESTs and 50 genomic sequences of B. mori. Since ESTs are a large collection, information is stored with respect to their cDNA library clone names (based on the annotation from http://www.ab.a.u-tokyo.ac.jp/silkbase/).

The extraction of microsatellite repeats is done using Simple Sequence Repeat Finder (SSRF) program (www.cdfd.org.in/micas), which is written in C.The primers for about 200 loci, which are experimentally tested, are stored in the PrimerBase, with their respective PCR amplification conditions.

The user-friendly interface for the database has been developed using PHP, a server side scripting language. This acts as a comprehensive and integrated resource for retrieval of the information from SilkSatDb. The user can query for microsatellites, extracted from WGS and EST sequences, using the repeat type/motif and the number of occurrence of the repeat.