ChickVD: a sequence variation database for the chicken genome.
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.
Wang
Jing
J
College of Life Sciences, Peking University, Beijing 100871, China.
He
Ximiao
X
Ruan
Jue
J
Dai
Mingtao
M
Chen
Jie
J
Zhang
Yong
Y
Hu
Yafeng
Y
Ye
Chen
C
Li
Shengting
S
Cong
Lijuan
L
Fang
Lin
L
Liu
Bin
B
Li
Songgang
S
Wang
Jian
J
Burt
David W
DW
Wong
Gane Ka-Shu
GK
Yu
Jun
J
Yang
Huanming
H
Wang
Jun
J
D000818:Animals; D002645:Chickens / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005260:Female; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D008297:Male; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface