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SilkDB: a knowledgebase for silkworm biology and genomics

2004; Oxford University Press; Volume: 33; Issue: Database issue Linguagem: Inglês

10.1093/nar/gki116

1362-4962

Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Ye Chen, Cheng-Wei Lü, Jun Wang, Songgang Li, Gane Ka‐Shu Wong, Huanming Yang, Jian Wang, Xiang Zhonghuai, Zeyang Zhou, Jun Yu,

Viral Infectious Diseases and Gene Expression in Insects

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 mandarina , 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. SilkDB is publicly accessible at http://silkworm.genomics.org.cn .