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2008-Gallus GBrowse a unified genomic database for the chicken.pdf

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2008-Gallus GBrowse a unified genomic database for the chicken

Published online 11 October 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D719–D723 doi:10.1093/nar/gkm783 Gallus GBrowse: a unified genomic database for the chicken Carl J. Schmidt1,*, Michael Romanov2, Oliver Ryder2, Vincent Magrini3, Matthew Hickenbotham3, Jarret Glasscock3, Sean McGrath3, Elaine Mardis3 and Lincoln D. Stein4 1Department of Animal and Food Sciences, University of Delaware, Newark, DE 19706, 2Conservation and Research for Endangered Species, Zoological Society of San Diego, San Diego, CA 92112-0551, 3Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108 and 4Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY 11724, USA Received August 10, 2007; Revised September 12, 2007; Accepted September 17, 2007 ABSTRACT Gallus GBrowse (/cgi-bin/ gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray probes, and mappings from turkey, condor and zebra finch DNA and EST sequences to the chicken genome. We also provide a BLAT server (/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species. INTRODUCTION The chicken (Gallus gallus) has played important roles in both scientific research and the general health and welfare of humans. For example, in the field of develop- mental biology, the chicken embryo model has provided insight into many developmental processes including cell migration (1–3), limb development (4,5) and eye forma- tion (6–8). The discovery of avian oncogenic viruses helped highlight the importance of specific genes in tu