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Nucleic Acids Research Advance Access published online on September 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp801
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology

Jun Duan1,2, Ruiqiang Li3, Daojun Cheng1, Wei Fan3, Xingfu Zha1, Tingcai Cheng1,2, Yuqian Wu2, Jun Wang3, Kazuei Mita4, Zhonghuai Xiang1 and Qingyou Xia1,2,*

1The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, 2The Institute of Agriculture and Life Sciences, Chongqing University, Chongqing 400030, 3Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 4National Institute of Agrobiological Sciences, Owashi 1-2, Tsukuba 305-8634, Japan

*To whom correspondence should be addressed. Tel: +86 23 68250099; Fax: +86 23 68251128; Email: xiaqy{at}swu.edu.cn

Received June 8, 2009. Revised August 11, 2009. Accepted September 13, 2009.

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.


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