Databases

Chicken Genome Sequence

• Ensembl Chicken Genome Browser
• University of California, Santa Cruz's Genome Browser - chicken genome browser gateway
• NCBI Map Viewer - chicken genome resources
• Genome Sequencing Center (WSHU) - at Washington University Medical School and focuses on the large scale generation and analysis of DNA sequence
• Trace Archive - developed to store the raw data underlying all of the sequence generated by the genome project
• Esembl Trace Server - provides a permanent archive for single pass DNA sequencing reads and associated traces and quality values
• Trace BLAST - Trace Archive searches with discontiguous Mega BLAST. This page is optimized for cross-species comparisons
• Chicken Genomic Sequencing Project Home Page - Sanger Institute, UK
• Genome Hub - National Human Genome Research Institute

EST Databases

• DT40 - intended to distribute materials and information among groups using DT40. Of particular interest can be the Bursal EST Database which may contain your gene as a cDNA sequence
• TIGR Gene Indices - Gallus gallus gene index
• UDEL Chicken ESR database - contains over 40,000 EST sequences from the chicken cDNA libraries in the UD collection
• University of Delaware chicken genes and annotations - ChickDB, HVDB and GoFigure
• UMIST - contains data from the UMIST/Nottingham/Dundee universities chicken EST sequencing project. 340,000 ESTs were sequenced from 21 different chicken tissues (both adult and foetal)
• dbEST - NCBI Expressed Sequence Tags database

SNP Databases

• ChickenVD: the chicken variation database
• UMIST - contains data from the UMIST/Nottingham/Dundee universities chicken EST sequencing project. A set of 11,000 high-confidence single nucleotide polymorphisms (SNPs) have been predicted using various filtering criteria and the Polybayes program.

Physical Mapping Databases

• ChickRH - RH mapping on INRA Chicken Radiation Hybrid panel.

Genes and Proteins

• Gene Ontology (GO) - The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing
• GeneCards - database of human genes, their products and their involvement in diseases
• Pfam (Sanger) - large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
• Antimicrobial Peptide & Protein Database (APPDb) - Bioinformatics Research Group, Education & Research Centre, St. Vincent's University Hospital, Elm Park, Dublin 4
• Encyclopedia of Life (EOL) - provides putative domain-based structure and functional annotation for publically available proteome data - chicken data

Genome Mapping Databases

• Arkdb (Roslin node) - The ARKdb database system provides comprehensive public repositories for genome mapping data from farmed and other animal species
• Arkdb (USDA node)
• ACEBrowser - Animal Sciences Group (Wageningen)

Other Avian Genomes

• Single locus traits of the turkey - provides in a graphic format, colored photographic images where possible, the various phenotypic expressions of single gene mutations and other genetic conditions that have been described in the turkey which may have economic significance
• Turkey Genome Mapping Database - part of the ARKdb family of genome mapping databases
• Turkey Genome Project - University of Minnesota Turkey Genome Project
• Quail Genetic Resource Center Home Page - University of British Columbia, Canada

Viral, Microbial and Parasite Genomes

• DOE Microbial Genome Programme - U.S. Department of Energy (DOE) Microbial Genome Program (MGP)
• Microbial Genomics Gateway - an overview of these efforts to sequence microbial genomes, potentially unlocking beneficial applications in bioremediation, climate change, biotechnology, energy production, and other vital areas
• Parasite genome databases - Parasite genome databases and genome research resources
• Parasites - Parasite Databases of Clustered ESTs
• Salmonella - provides information on sequencing the Salmonella genome and other resources
• Viral Genome Organizer - an overview of these efforts to sequence microbial genomes, potentially unlocking beneficial applications in bioremediation, climate change, biotechnology, energy production, and other vital areas
• Microbes.info - designed to bring useful and interesting microbiology informational resources to you. Allows effective, efficient searching for any information. This web site attempts to reduced the clutter and the size of the haystack in an effort to help you filter through the information in an organized manner.

Non-Avian Genomes

• Arkdb - The ARKdb database system provides comprehensive public repositories for genome mapping data from farmed and other animal species
• Ensembl - presents up-to-date sequence data and the best possible automatic annotation for metazoan genomes. Available now are human, mouse, rat, fugu, zebrafish, mosquito, Drosophila, C. elegans, and C. briggsae, Others will be added soon.
• Vega - Vertebrate Genome Annotation (VEGA) database is designed to be a central repository for manual annotation of different vertebrate finished genome sequence.
• MGI - Mouse Genome Informatics
• NCBI - National Center for Biotechnology Information
• TIGR - The Institute for Genomic Research

Other Genome Links

• Sequence Repositories - links to organism-specific genomic and transcriptomi resources
• Complete Genomes - list of completed genome sequences
• Animal Genome Size Database - a comprehensive catalogue of animal genome size data

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