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ChickVD


NAR Molecular Biology Database Collection entry number 647
Wang J.1, He X.2,3, Ruan J.2,3, Dai M.2, Chen J.2, Zhang Y.1,2, Hu Y.2, Ye C.2, Li S.2, Cong L.2, Fang L.2, Liu B.2, Li S.1,2, Wang J.2, Burt D.W.4, Wong G.K.-S.2,5, Yu J.2,6, Yang H.2,6 and Wang J.1,2,7,8
1College of Life Sciences, Peking University, Beijing 100871, China,
2Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone B-6, Beijing 101300, China,
3Graduate School of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100039, China,
4Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK,
5University of Washington Genome Center, Department of Medicine, Seattle, WA 98195, USA,
6James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China,
7The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark and
8Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark

Database Description

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, 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 (QTL) using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches.

Acknowledgements

This project was funded by the Chinese Academy of Sciences, Commission for Economy Planning, Ministry of Science and Technology (2002AA104250, 2002AA234011, 2001AA231061, 2001AA231011, 2001AA231101 and 2004AA231050), Danish National Research Foundation (Danish Platform for Integrative Biology) and the China National Grid (2002AA104250).

References

Wang J, He X, Ruan J, Dai M, Chen J, Zhang Y, Hu Y, Ye C, Li S, Cong L, Fang L, Liu B, Li S, Wang J, Burt DW, Wong GK, Yu J, Yang H, Wang J. ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 2005, 33: D438-D441.


Go to the abstract in the NAR 2005 Database Issue.
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