Online Research Resources

Online Research Resources

• From NHGRI
  • Online Research Resources Developed at NHGRI
  • NHGRI Reports and Publications
  • The NHGRI Genome Sequencing Program (GSP)
• Beyond NHGRI
  • The Completed Human Sequence
  • Other Federal Agencies Involved in Genomics
  • Human Genome Sequence Assemblies and Other Genomic Data Resources
  • Underlying Map Information
  • Sequencing Centers of the International Human Genome Sequencing Consortium
  • Model Organism Genome Projects
    • Archaea and Bacteria
    • Eukaryotes
  • Databases
    • National Center for Biotechnology Information (NCBI) Databases and Tools
    • Nucleotide Sequence Databases
    • Trace Archives (Raw Sequence Data Repositories)
    • Single Nucleotide Polymorphisms (SNPs)
    • cDNAs and Expressed Sequence Tags (ESTs)
    • Model Organism Databases
    • Additional Sequence, Gene and Protein Databases
  • Ethical, Legal and Social Implications (ELSI) Information
  • Funding Agencies
  • Additional Genome Resources
  • Biology Resources
  • Selected Journals

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

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

The NHGRI Genome Sequencing Program (GSP)
Genome sequencing projects currently in production and funded by NHGRI.

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 Agencies 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 [useast.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 [w3.genethon.fr/php/index_us.php]

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 [broadinstitute.org]
  (Now the Broad Institute of MIT and Harvard)
• 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 [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 [genomics.cn]
• Stanford Genome Technology Center [med.stanford.edu]
• HudsonAlpha Genome Sequencing Center [hagsc.org/]
• University of Washington Genome Center [gs.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 [mccombielab.cshl.edu]
• GBF: German Research Centre for Biotechnology [helmholtz-hzi.de]

Model Organism Genome Projects

Archaea and Bacteria

• J. Craig Venter Institute [jcvi.org]
• The Sanger Institute - Bacterial Genomes [sanger.ac.uk]
• Bacillus subtilis Genome [bacillus.genome.ad.jp]
• E. coli Genome Project [genome.wisc.edu]

Eukaryotes

• The Arabidopsis Information Resource (TAIR) [arabidopsis.org]
• C. elegans Genome Project [sanger.ac.uk]
• 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 [yeastgenome.org]
• The Zebrafish Model Organism Database [zfin.org]

Databases

National Center for Biotechnology Information (NCBI) Databases and Tools

• NCBI [ncbi.nlm.nih.gov]
• EntrezGene [ncbi.nlm.nih.gov]
  A searchable database of genes
• NCBI Reference Sequence Project (RefSeq) [ncbi.nlm.nih.gov]
• Macromolecular 3D Structures Database (MMDB) [ncbi.nlm.nih.gov]
• GenBank [ncbi.nlm.nih.gov]

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)

• 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 [osc.riken.go.jp]

Model Organism Databases

• Berkeley Drosophila Genome Project [fruitfly.org]
• Ciona savigny Database [broadinstitute.org]
• FlyBase, Drosophila Database [flybase.bio.indiana.edu]
• MGD, The Mouse Genome Database [informatics.jax.org]
• Saccharomyces Genome Database [yeastgenome.org]
• Tetraodon nigroviridis Database [broadinstitute.org]
• WormBase, The C. elegans Genome Database [wormbase.org]
• Gene Ontology Consortium [geneontology.org]
• The Generic Model Organism Project (GMOD) [gmod.org]

Additional Sequence, Gene and Protein Databases

• InterPro protein sequence analysis & classification [ebi.ac.uk]
  An integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes.
• Eukaryotic Promoter Database [epd.isb-sib.ch]
• PROSITE [expasy.org]
  A database of protein families and domains.
• SWISS-PROT [web.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 [swift.cmbi.ru.nl]
  A database of secondary structure protein assignments.
• FSSP [biocenter.helsinki.fi]
  A database of fold classifications based on structure-structure alignment of proteins.
• Nucleic Acid Database Project (NDB) [ndbserver.rutgers.edu]
  Structural information about nucleic acids.
• The I.M.A.G.E. Consortium [image.hudsonalpha.org]
  A public collection of genes.

Ethical, Legal and Social Implications (ELSI) Research Program

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

Funding Agencies

• National Human Genome Research Institute Grants
• Department of Energy Human Genome Program [genomics.energy.gov]
• 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 [ars.usda.gov]
  Cooperative State Research, Education and Extension Service [csrees.usda.gov]

Additional Genome Resources

• Basic Local Alignment Search Tool (BLAST) [blast.ncbi.nlm.nih.gov]
• NCBI Genomes Guide [ncbi.nlm.nih.gov]
• Ensembl Genome Browser Explore the Human Genome [ensembl.org]

Biology Resources

• Entrez Cross-database Search [ncbi.nlm.nih.gov]
• PubMed Biomedical Literature Database [ncbi.nlm.nih.gov]

Selected Journals

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

Last Updated: February 27, 2017