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.

[1]  Damian Smedley,et al.  Ensembl 2004 , 2004, Nucleic Acids Res..

[2]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[3]  Olivier Pourquié,et al.  Chicken Genome--Science Nuggets to Come Soon , 2003, Science.

[4]  G. Rubin,et al.  A computer program for aligning a cDNA sequence with a genomic DNA sequence. , 1998, Genome research.

[5]  David L. Wheeler,et al.  GenBank: update , 2004, Nucleic Acids Res..

[6]  Jörg Männer,et al.  A chicken model to study the embryology of cloacal exstrophy. , 2003, Journal of pediatric surgery.

[7]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[8]  Jian Wang,et al.  BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics , 2004, Nucleic Acids Res..

[9]  Paul E. Boardman,et al.  A Comprehensive Collection of Chicken cDNAs , 2002, Current Biology.

[10]  Paul E Mozdziak,et al.  Status of transgenic chicken models for developmental biology , 2004, Developmental dynamics : an official publication of the American Association of Anatomists.

[11]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[12]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[13]  Mary Ann Ottinger,et al.  Birds as long-lived animal models for the study of aging , 2003, Experimental Gerontology.

[14]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[15]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[16]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .