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Genomics Databases
Author: Warren Lathe
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"Database URL Repositories NCBI (GenBank) http://www.ncbi.nlm.nih.gov/ EMBL-EBI http://www.ebi.ac.uk/ DDBJ http://www.ddbj.nig.ac.jp/ INSDC http://www.insdc.org/ RefSeq http://www.ncbi.nlm.nih.gov/RefSeq/ VEGA http://vega.sanger.ac.uk/ CCDS http://www.ncbi.nlm.nih.gov/CCDS/ Genome Browsers Ensembl http://www.ensembl.org/ UCSC Genome Browser http://genome.ucsc.edu/ NCBI MapViewer http://www.ncbi.nlm.nih.gov/mapview/ Projects (in Genome Browsers section) ENCODE (project) http://www.genome.gov/10005107 1000 Genomes http://www.1000genomes.org/ Species & Taxa specific databases Rat Genome Database http://rgd.mcw.edu/ Mouse Genome Informatics http://www.informatics.jax.org/ ZFIN, Zebrafish Model Organism Database http://zfin.org FlyBase, Drosophila and other species http://flybase.org/ VectorBase, invertebrate vectors of human disease http://www.vectorbase.org/ WormBase, C. elegans and related nematodes http://www.wormbase.org Gramene, crop grasses and other plants http://www.gramene.org TAIR, Arabidopsis http://www.arabidopsis.org/ SGD, Saccharomyces Genome Database http://www.yeastgenome.org/ IMG, Integrated Microbial Genomes http://img.jgi.doe.gov/ EcoliHub, community and database for E. coli http://www.ecolicommunity.org/ VBRC, Viral Bioinformatics Resource Center http://athena.bioc.uvic.ca/ GMOD, Genome Database Tools (and databases using GMOD) GMOD http://gmod.org/ HGSDD, Human Genome Segmental Duplication Database http://projects.tcag.ca/humandup/ HapMap http://www.hapmap.org James Watson Genome http://jimwatsonsequence.cshl.edu/ List of Additional GMOD uses http://gmod.org/wiki/GMOD_Users Subject-Specific Databases PDB, Protein 3D structure Database http://www.rcsb.org/ Pfam, protein families http://pfam.sanger.ac.uk/ GEO, Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ ArrayExpress, repository for transcriptomics data http://www.ebi.ac.uk/microarray-as/ae/ dbGaP http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap HuGE Navigator http://www.hugenavigator.net/ Additional Databases Directory Nucleic Acids Research Database Directory http://nar.oxfordjournals.org/cgi/content/full/gkm10 37/DC1 Discussion: Learning the Genome Browsers Ensembl Online Workshops http://www.ensembl.org/common/Workshops_Onli ne UCSC Genome Browser Tutorial http://www.openhelix.com/ucsc NCBI MapViewer Introduction http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=han dbook.chapter.ch20 Table 1: A list of database and their URLs mentioned in the article. Table is organized with similar headings found in the article and lists resources mentioned and URLs. As mentioned in the article, there are hundreds more databases and resources available to the researcher. A link to the 2008 NAR database directory is given. Additionally, three links to introductory training for the 3 genome browsers is given to help the reader get started. "
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Genetics
Gene Inheritance and Transmission
Gene Expression and Regulation
Nucleic Acid Structure and Function
Chromosomes and Cytogenetics
Evolutionary Genetics
Population and Quantitative Genetics
Genomics
Genes and Disease
Genetics and Society
Cell Biology
Cell Origins and Metabolism
Proteins and Gene Expression
Subcellular Compartments
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Cell Cycle and Cell Division
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