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Online Research Resources

From NHGRI

Online Research Resources Developed at NHGRI
Software, databases and research project Web sites from NHGRI's Division of Intramural Research (DIR).

NHGRI Reports and Publications

• Reports and Publications from the Division of Extramural Research:
  Workshops and priority setting reports, long-range planning, and Ethical, Legal, and Social Implications (ELSI) reports
  
  
• Books and Publications from the Division of Intramural Research:
  Scientific publications by NHGRI investigators, genomics course materials, and program publications

Sequences, Maps and BAC Libraries
Genome sequencing and BAC library proposals and projects currently in production and funded by NHGRI.

Includes:

• Requests for Development of New Genomic Resources
• BAC Library Proposals and Information
• The BAC Resource Network

Beyond NHGRI

The Completed Human Sequence:

• At the National Center for Biotechnology Information (NCBI) [ncbi.nlm.nih.gov]
  
  
• At the University of California Santa Cruz (UCSC) Gateway [genome.cse.ucsc.edu]
  
  
• At Ensembl [ensembl.org]

Other Federal Projects Involved in Genomics

Human Genome Sequence Assemblies and Other Genomic Data Resources

• UCSC Human Genome Browser Gateway [genome.cse.ucsc.edu]
• Ensembl Human Genome Server [ensembl.org]
• NCBI Human Genome Guide [ncbi.nlm.nih.gov]
• Oak Ridge National Laboratory's Genome Channel [compbio.ornl.gov]

Underlying Map Information

• GeneMap99 [ncbi.nlm.nih.gov]
• Marshfield Comprehensive Human Genetic Maps [research.marshfieldclinic.org]
• Genethon [genethon.fr]
• Radiation Hybrid Database (RHdb) [corba.ebi.ac.uk]

Sequencing Centers of the International Human Genome Sequencing Consortium

(Listed in order of total sequence contributed to the draft human sequence published February 15, 2001, Nature 409, 860-921)

• Whitehead Institute for Biomedical Research Center for Genome Research [genome.wi.mit.edu]
  (Now the Broad Institute/MIT Center for Genome Research)
• The Sanger Institute [sanger.ac.uk]
• Washington University Genome Sequencing Center [genome.wustl.edu]
• US DOE Joint Genome Institute [jgi.doe.gov]
• Baylor College of Medicine Human Genome Sequencing Center [hgsc.bcm.tmc.edu]
• RIKEN Genomic Sciences Center [hgp.gsc.riken.go.jp]
• Genoscope [genoscope.cns.fr]
• GTC Sequencing Center [genomecorp.com]
  (Now Oscient Pharmaceuticals)
• Department of Genome Analysis, Institute of Molecular Biotechnology [genome.imb-jena.de]
• Multimegabase Sequencing Center, The Institute for Systems Biology [systemsbiology.org]
• Beijing Genomics Institute Human Genome Center [btn.genomics.org.cn]
• Stanford Genome Technology Center [sequence-www.stanford.edu]
• Stanford Human Genome Center [shgc-www.stanford.edu]
• University of Washington Genome Center [genome.washington.edu]
• Department of Molecular Biology, Keio University School of Medicine [dmb.med.keio.ac.jp]
• University of Texas Southwestern Medical Center at Dallas [utsouthwestern.edu]
• University of Oklahoma's Advanced Center for Genome Technology [genome.ou.edu]
• Max Planck Institute for Molecular Genetics [seq.molgen.mpg.de]
• Cold Spring Harbor Laboratory, Lita Annenberg Hazen Genome Center [nucleus.cshl.org]
• GBF--German Research Centre for Biotechnology [genome.gbf.de]

Model Organism Genome Projects

Archaea and Bacteria

• The Institute for Genomic Research (TIGR) Microbial Database [tigr.org]
  A listing of published microbial genomes and chromosomes and those in progress.
• The Sanger Institute Microbial Sequencing Projects [sanger.ac.uk]
• Bacillus subtilis Genome [pbil.univ-lyon1.fr]
• E. coli Genome Project [genome.wisc.edu]

Eukaryotes

• The Arabidopsis Information Resource (TAIR) [arabidopsis.org]
• C. elegans Genome Project [sanger.ac.uk]
• Candida albicans information [alces.med.umn.edu]
• Dog Genome Project [mendel.berkeley.edu]
• Flybase [flybase.bio.indiana.edu]
• Fugu Genomics Project [fugu.hgmp.mrc.ac.uk]
• Fungal Genome Resource [gene.genetics.uga.edu]
• Maize Genome Database (ZmDB) [maizegdb.org]
• Mouse Genome Informatics [informatics.jax.org]
• Pneumocystis Genome Project [biology.uky.edu]
• Rice Genome Research Program [rgp.dna.affrc.go.jp]
• Saccharomyces Genome Database [stanford.edu]
• The Zebrafish Information Network [zfin.org]

Databases

National Center for Biotechnology Information (NCBI) Databases and Tools

• NCBI [ncbi.nlm.nih.gov]
• LocusLink [ncbi.nlm.nih.gov]
  A genetic loci information resource.
• NCBI Reference Sequence Project (RefSeq) [ncbi.nlm.nih.gov]
• Macromolecular 3D Structures Database (MMDB) [ncbi.nlm.nih.gov]
• GenBank [ncbi.nlm.nih.gov]
• The Genome Database [gdb.org]

Nucleotide Sequence Databases

• GenBank [ncbi.nlm.nih.gov]
• EMBL Nucleotide Sequence Database [ebi.ac.uk]
• DNA Data Bank of Japan [ddbj.nig.ac.jp]

Trace Archives (Raw Sequence Data Repositories)

• Ensemble Trace Server [trace.ensembl.org]
• NCBI Trace Archive [ncbi.nlm.nih.gov]

Single Nucleotide Polymorphisms (SNPs)

• The SNP Consortium [snp.cshl.org]
• NCBI dbSNP [ncbi.nlm.nih.gov]

cDNAs and Expressed Sequence Tags (ESTs)

• Mammalian Gene Collection [mgc.nci.nih.gov]
• NCBI dbEST [ncbi.nlm.nih.gov]
• RIKEN Mouse Encyclopedia [genome.rtc.riken.go.jp]

Model Organism Databases

• Berkeley Drosophila Genome Project [fruitfly.org]
• Ciona savigny Database [genome.wi.mit.edu]
• FlyBase, Drosophila Database [flybase.bio.indiana.edu]
• MGD, The Mouse Genome Database [informatics.jax.org]
• SGD, Saccharomyces Genome Database [stanford.edu]
• Tetraodon nigroviridis Database [genome.wi.mit.edu]
• WormBase, The C. elegans Genome Database [wormbase.org]
• Gene Ontology Consortium [geneontology.org]
• The Generic Model Organism Project (GMOD) [gmod.org]
• TIGR Databases and Comprehensive Microbial Resource [tigr.org]
• Phytopthora Genome Consortium Database [pfgd.org/]

Additional Sequence, Gene and Protein Databases

• BLOCKS [blocks.fhcrc.org]
  A service for biological sequence analysis.
• Eukaryotic Promoter Database [epd.isb-sib.ch]
• PROSITE [expasy.org]
  A database of protein families and domains.
• SWISS-PROT [expasy.org]
  A protein knowledgebase.
• BioMagResBank [bmrb.wisc.edu]
  NMR spectroscopy data on proteins, peptides, and nucleic acids.
• Protein Data Bank (PDB) [rcsb.org]
  The repository for 3-D biological macromolecular structure data.
• DSSP [cmbi.kun.nl]
  A database of secondary structure protein assignments.
• FSSP [biocenter.helsinki.fi]
  A database of fold classifications based on structure-structure alignment of proteins.
• HSSP [cmbi.kun.nl]
  A database of homology-derived secondary structure of proteins.
• Nucleic Acid Database Project (NDB) [ndbserver.rutgers.edu]
  Structural information about nucleic acids.
• The I.M.A.G.E. Consortium [image.llnl.gov]
  A public collection of genes.

Ethical, Legal and Social Implications (ELSI) Information

• ELSI Research (NHGRI)
• Ethical, Legal and Social Issues (ELSI) [ornl.gov]
  Department of Energy (DOE)

Funding Agencies

• National Human Genome Research Institute
• Department of Energy Human Genome Program [doegenomes.org]
• The Wellcome Trust [wellcome.ac.uk]
• National Institutes of Health [nih.gov]
• National Science Foundation [nsf.gov]
• United States Department of Agriculture:
  Agricultural Research Service [nps.ars.usda.gov]
  Cooperative State Research, Education and Extension Service [reeusda.gov]

Additional Genome Resources

• Basic Local Alignment Search Tool (BLAST) [ncbi.nlm.nih.gov]
• NCBI Genomes Guide [ncbi.nlm.nih.gov]
• EBI/Sanger Institute Human Genome Central [ensembl.org]

Biology Resources

• Bio Online [synapse.bio.com]
• Biolinks [mcb.harvard.edu]
• Edinburgh School of Biology Genetics Glossary [helios.bto.ed.ac.uk]
• Entrez Search and Retrieval System [ncbi.nlm.nih.gov]
• PubMed Biomedical Literature Database [ncbi.nlm.nih.gov]

Selected Journals

• Cell [cell.com]
• Genome Research [genome.org]
• Journal of Biological Chemistry [jbc.org]
• Journal of Molecular Biology [sciencedirect.com]
• Nature [nature.com]
• Nature Genetics [nature.com]
• Science [sciencemag.org]

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Last Updated: June 2004