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Nucleic Acids Research 2005 33(Database Issue):D399-D402; doi:10.1093/nar/gki116
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Nucleic Acids Research, 2005, Vol. 33, Database issue D399-D402
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

SilkDB: a knowledgebase for silkworm biology and genomics

Jing Wang1, Qingyou Xia2, Ximiao He3,4, Mingtao Dai3, Jue Ruan3,4, Jie Chen3, Guo Yu3, Haifeng Yuan3, Yafeng Hu3, Ruiqiang Li3, Tao Feng3, Chen Ye3, Cheng Lu2, Jun Wang1,3,5, Songgang Li1, Gane Ka-Shu Wong3,6, Huanming Yang3,5, Jian Wang3,5, Zhonghuai Xiang2, Zeyang Zhou2 and Jun Yu3,5,*

1 College of Life Sciences, Peking University, Beijing 100871, China, 2 The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing, 400716, China, 3 Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China, 4 Graduate School of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100039, China, 5 Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou Genomics Institute, James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, China and 6 Department of Medicine, University of Washington Genome Center, Seattle, WA 98195, USA

* To whom correspondence should be addressed. Tel: +86 10 80481455; Fax: +86 10 80498676; Email: junyu{at}genomics.org.cn
Correspondence may also be addressed to Zeyang Zhou. Tel: +86 23 68251123; Fax: +86 23 68251128; Email: zyzhou{at}swau.cq.cn
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors

Received August 15, 2004; Revised and Accepted October 20, 2004

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.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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