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SilkSatDb


NAR Molecular Biology Database Collection entry number 744
Prasad, M.D.1, Muthulakshmi, M.1, Arunkumar, K.P.1, Madhu, M.1, Sreenu, V.B.2, Pavithra, V.2, Bose, B.2, Nagarajaram, H.A.2, Mita, K.3, Shimada, T.4 and Nagaraju, J.1
1Laboratories of Molecular Genetics and 2Computational Biology & Bioinformatics Facility (EMBnet India Node), Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad - 500076, India
3Insect genome, National Institute of Agrobiological sciences, Owashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
4Laboratory of Insect Genetics and Bioscience, Dept. of Agricultural and Environmental Biology, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.

Database Description

SilkSatDb is a comprehensive relational database of silkworm microsatellites that gives description of abundance, frequency and distribution of different classes of microsatellites in autosomes, Z-chromosome and expressed sequence tags (ESTs). Allelic and primer information for more than 250 validated microsatellites are given. The database hosts ESTs, Z-chromosome BACs (Bacterial Artificial Chromosomes) and whole genome shot-gun sequences. The database can be queried for different microsatellite motifs from these sequences. In addition, the database is interfaced to Autoprimer, a primer-designing program, which can be used to design primers for the loci of interest. The database hosts information on different types of mutations that are prevalent in different classes of microsatellite motif. The database is also provided with additional information on relevant protocols to carry out microsatellite marker analysis. The Primerbase is provided for all the validated microsatellite loci, which includes information on primer sequences along with PCR conditions for each of the primer sets. The data generated from SilkSatDb will be useful for the research community working on insect genetics, lepidopteran geneticists in particular across the globe. The links to different genetic resources of silkworm, Drosophila and Caenorhabditis elegans and microsateliite analyses tools are provided. The microsatellites in silkworm will help in initiating studies on population genetics, construction of molecular genetic and physical maps, marker assisted selection, in addition to understanding the basic biology of microsatellites. Studies on evolutionarily conservation of microsatellite loci of B. mori in other lepidopteran insects, which include some of the most destructive agricultural pests will augment resources for comparative genomics of these insects.

Acknowledgements

This work was supported by a grant from Department of Biotechnology, Govt. of India, New Delhi, to JN. HAN gratefully acknowledges the core grant support of CDFD. KPA and VBS are recipients of CSIR research fellowship. Authors acknowledge the help of Mrs. Geeta Thanu during the database creation.


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