title: ChickVD: a sequence variation database for the chicken genome.
abstract: 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.
authors.affiliation: College of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.forename: Mingtao
authors.initials: M
authors.lastname: Dai
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yafeng
authors.initials: Y
authors.lastname: Hu
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.forename: Shengting
authors.initials: S
authors.lastname: Li
authors.forename: Lijuan
authors.initials: L
authors.lastname: Cong
authors.forename: Lin
authors.initials: L
authors.lastname: Fang
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: 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