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Nucleic Acids Research 2005 33(Database Issue):D438-D441; doi:10.1093/nar/gki092
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Nucleic Acids Research, 2005, Vol. 33, Database issue D438-D441
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

ChickVD: a sequence variation database for the chicken genome

Jing Wang1, Ximiao He2,3, Jue Ruan2,3, Mingtao Dai2, Jie Chen2, Yong Zhang1,2, Yafeng Hu2, Chen Ye2, Shengting Li2, Lijuan Cong2, Lin Fang2, Bin Liu2, Songgang Li1,2, Jian Wang2, David W. Burt4, Gane Ka-Shu Wong2,5, Jun Yu2,6, Huanming Yang2,6 and Jun Wang1,2,7,8,*

1 College of Life Sciences, Peking University, Beijing 100871, China, 2 Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone B-6, Beijing 101300, China, 3 Graduate School of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100039, China, 4 Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK, 5 University of Washington Genome Center, Department of Medicine, Seattle, WA 98195, USA, 6 James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China, 7 The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark and 8 Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark

* To whom correspondence should be addressed. Tel: +86 10 80481662; Fax: +86 10 80498676; Email: wangj{at}genomics.org.cn
Correspondence may also be addressed to Huanming Yang. Tel: +86 10 80494969; Fax: +86 10 80491181; Email: yanghm{at}genomics.org.cn
The authors wish it to be known that, in their opinion, the first two authors should be regarded as First Authors

Received August 14, 2004; Revised and Accepted October 12, 2004

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the ‘Chicken Variation Database’ (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.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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