SPICEST-Annotated SPICE EST database
Discovering SSRs,SNPs, Primers and Genes

Spices SSRs
SNP Results
Primer Results
Est Annotation
Gene Search
Welcome to Spice EST database

  SpicEST -Spices EST Annotation Database is consist of two spice like turmeric and ginger EST database and SNP database. It can be accessible through online. EST Data records were downloaded from NCBI open source database. All EST records for curcuma longa and zingiber officinale were mined and stored in MYSQL database. These ESTs were assembled using sequence assembly programme like CAP3. Contigs results were provided in the database. This EST records were separated as a tissue based EST libraries and furthur analysed and the results were stored in the databases. By searching and navigating the menus we can reterive the results of identified SSRs from EST with five different SSR identification tools - MISA, ETRA,SSR PRIMER, SSRIT and WEB TROLL (for both curcuma and Zingiber). Using this SSRepeat target primers were desingned by PRIMER3 software and primer quality were checked using FAST PCR. These primers results can be reterived from the database. Primers are being validated in wetlab. All ESTs of both spices were annotated using ESTPASS server. These results were used to find the putative gene and metabolic pathway.

SpiceSNIP database is developed for both spices turmeric and ginger or else this database can be called as Mined SNPs from EST libraries of curcuma longa and zingiber officinale. In this database two programs like CAP3 and AUTOSNP are used for analysis. SNP results can be retrieved by clicking the list of contigs, which is derived from curcuma leaves and rhizomes ESTs provided with transition, transversion and indel polymorphism.

This 'SpicEST' database would help the scientific community those who are working on turmeric and ginger. The result of this study has many practical implications for curcuma and Zingiber breeders.


Designed and Developed by: Chandrasekar A., Riju A., Sathyanath V and S.J. Eapen, Bioinformatics Centre, IISR, Calicut.