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SilkDB


NAR Molecular Biology Database Collection entry number 743
Wang J.1, Xia Q.2, He X.3,4, Dai M.3, Ruan J.3,4, Chen J.3, Yu G.3, Yuan H.3, Hu Y.3, Li R.3, Feng T.3, Ye C.3, Lu C.2, Wang J.1,3,5, Li S.1, Wong G.K.-S.3,6, Yang H.3,5, Wang J.3,5, Xiang Z.2, Zhou Z.2 and Yu J.3,5
1College of Life Sciences, Peking University, Beijing 100871, China,
2The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing, 400716, China,
3Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China,
4Graduate School of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100039, China,
5Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou Genomics Institute, James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, China and
6Department of Medicine, University of Washington Genome Center, Seattle, WA 98195, USA

Database Description

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration, and study of silkworm genetic and genomic data. With the recent accomplishment of a ~6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarinai, a wild progenitor of B. mori , and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B. mori and other Lepidoptera, and between B. mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B. mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies.

Acknowledgements

This project was funded by Chinese Academy of Sciences (KSCX2-SW-223), National Development and Reform Commission, Ministry of Science and Technology (2002AA104250; 2002AA234011; 2001AA231061; 2001AA231011; 2001AA231101; 2004AA231050; 30200163; 90208019), China National Grid (2002AA104250) and 863 High Technology Foundation of China (2004AA2Z1020).

References

Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R, Feng T, Ye C, Lu C, Wang J, Li S, Wong GK, Yang H, Wang J, Xiang Z, Zhou Z, Yu J. SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res. 2005, 33: D399-D402.


Go to the abstract in the NAR 2010 Database Issue.
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