Major Genome Browsers
Ensembl http://www.ensembl.org
NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/
UCSC Genome Browser http://genome.ucsc.edu
Additional Genome Browsers
In addition to the genome browsers discussed in this Guide, the reader may find these additional views of the human genome sequence helpful. Each of these sites provides documentation on their scope of coverage and how to examine the data housed at that site.
ORNL Genome Channel http://compbio.ornl.gov/channel/
RIKEN Genomic Sciences Center http://hgrep.ims.u-tokyo.ac.jp/
Genome annotation
The following sites provide detailed information on annotations at each of the three major genome portals.
Distributed Annotation System http://www.ensembl.org/Docs/wiki/html /EnsemblDocs/EnsemblDAS.html
Ensembl Science Documentation http://www.ensembl.org/Docs/wiki/html /EnsemblDocs/ScienceDocumentation.html
NCBI Contig Assembly and Annotation Process http://www.ncbi.nlm.nih.gov/genome/guide /build.html
UCSC Annotation Database http://genome.ucsc.edu/goldenPath/help/ hgTracksHelp.html
Human Genome Hub and Genome Central
These sites provide jumping-off points to major genome-based web sites. Resources available include trace data archives, access to cDNA and expressed sequence tag data and mapping information used to produce genome assemblies. The web sites of the individual members of the International Human Genome Sequencing Consortium may be accessed through these sites.
Ensembl Human Genome Central http://www.ensembl.org/genome/central/
NCBI Human Genome Central http://www.ncbi.nlm.nih.gov/genome/guide/central.html
NHGRI Genome Hub http://www.nhgri.nih.gov/genome_hub.html
UK HGMP GenomeWeb http://www.hgmp.mrc.ac.uk/GenomeWeb /genome-db.html
Major public sequence databases
Each of these databases belongs to the International Nucleotide Sequence Database Collaboration. Although all three centers provide separate mechanisms for sequence submission by individual investigators, they exchange data daily. As each member database stores and presents the underlying data using a slightly different format, this data exchange makes all known nucleotide and protein sequence data available to all users, regardless of which of the three databases are queried.
DNA Data Bank of Japan http://www.ddbj.nig.ac.jp
EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/index.html
GenBank http://www.ncbi.nlm.nih.gov
Expressed sequence tag clustering databases
The ability to bring together expressed sequence tag, mRNA and other related sequences into gene-oriented clusters often facilitates genomic analysis, since the method groups individual sequences that most likely arise from the same gene or transcript. These three databases provide gene-oriented views of the data, using different algorithms in calculating the individual gene clusters.
TIGR Gene Indices http://www.tigr.org/tdb/tgi.shtml
Human genetic and physical maps
The databases listed below represent a significant portion of the data underlying current human genome assemblies. Many of these data are available through DDBJ/EMBL/GenBank, but each database contains additional information regarding clones, constructs and similar that is not available through the major sequence repositories. A more extensive list of human genetic and physical maps can also be found through the online Nucleic Acids Research Database Collection, at http://nar.oupjournals.org/cgi/content/full/30/1/1/DC1.
Bacterial artificial chromosome and accession maps http://genome.wustl.edu/projects/human/index.php?fpc=1
GenAtlas http://www.citi2.fr/GENATLAS/
Genebridge4 radiation hybrid maps http://www.sanger.ac.uk/Software/RHserver /RHserver.shtml
GeneMap '99 http://www.ncbi.nlm.nih.gov/genemap99
Généthon linkage map http://www.genethon.fr/index_en.html
Marshfield genetic maps http://research.marshfieldclinic.org/genetics /Map_Markers/maps/IndexMapFrames.html
Stanford G3 and TNG radiation hybrid maps http://www-shgc.stanford.edu/RH/
Genomic Databases and Resources
In addition to the databases listed in the section above, there are numerous useful databases containing human mutation, variation, medical or expression data. This short list is offered as a representative cross-section of the types of database freely available to genome researchers. The reader is referred to the 'lists of lists' found at the Human GenomeHub and Genome Central cites for a more extensive catalog of available resources.
Cancer Genome Anatomy Project (CGAP) http://www.ncbi.nlm.nih.gov/CGAP/
Genome DataBase (GDB) http://www.gdb.org
HUGO Gene Nomenclature http://www.gene.ucl.ac.uk/nomenclature
Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/Omim
SNP Consortium http://snp.cshl.org
Sequence-based searching
The following links provide access to the most frequently used tools for performing sequence-based comparisons to human genome data. An extensive list of sequence similarity search tools can be found on the ExPASy web site, at http://us.expasy.org/tools/.
Ensembl BLAST http://www.ensembl.org/Homo_sapiens/blastview
Model organism databases
This list represents a small subset of the sequencing initiatives on model organisms. Additional information on the progress of numerous model organism sequencing initiatives can be found on the Model Organisms for Biomedical Research web page, at http://www.nih.gov/science/models/. A more extensive list of organismal databases can also be found through the online Nucleic Acids Research Database Collection, at http://nar.oupjournals.org/cgi/content/full/30/1/1/DC1.
Arabidopsis thaliana
The Arabidopsis Information Resource http://www.arabidopsis.org
Arabidopsis Genome Initiative http://mips.gsf.de/proj/thal/db/
Caenorhabditis elegans
AceDB http://www.acedb.org
WormBase http://www.wormbase.org/
Drosophila melanogaster
Berkeley Drosophila Genome Project http://www.fruitfly.org/
FlyBase http://flybase.bio.indiana.edu/
Escherichia coli
Microbial Genomes
Comprehensive Microbial Resource http://www.tigr.org/tigr-scripts/CMR2 /CMRHomePage.spl
TIGR Microbial Database http://www.tigr.org/tdb/mdb/
Mouse
Mouse Genome Database/Informatics http://www.informatics.jax.org/
Rat
Rat Genome Database http://rgd.mcw.edu
Yeast
Comprehensive Yeast Genome Database http://mips.gsf.de/proj/yeast/CYGD/db/
Saccharomyces Genome Database http://genome-www.stanford.edu/Saccharomyces/
S. pombe Genome Sequencing Project http://www.sanger.ac.uk/Projects/S_pombe/
Zebrafish Zebrafish Information Network http://zfin.org
Ethical, legal and social Issues
Although this guide has focused on the mechanics of accessing and using human genome data, it is important to remember that ethical, legal and social issues (ELSI) are becoming increasingly important in this age of genetic and genomic research. The following web sites provide an introduction to important issues related to genome biology as applied to human health and provide a jumping-off point for further information.
DOE ELSI Program http://www.ornl.gov/hgmis/elsi/elsi.html
Lawrence Berkeley National Laboratory http://www.lbl.gov/Education/ELSI/
NHGRI ELSI Program http://www.nhgri.nih.gov/ELSI/
Genetic education
The following sites present basic information on genetics and genomics, much of which is appropriate for elementary and secondary school education, as well as for the college level. Many of these sites offer teaching plans, graphics and other teaching resources that can be freely used in the classroom or lecture hall.
Access Excellence http://www.accessexcellence.org/
Department of Energy education resources http://www.ornl.gov/hgmis/education/education.html
Genetics Education Center http://www.kumc.edu/gec/
NHGRI Exploring our Molecular Selves Multimedia Kit http://www.genome.gov/Pages/EducationKit/
NHGRI Glossary of Genetic Terms http://www.genome.gov/glossary.cfm
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Web resources: Internet resources featured in this guide. Nat Genet 35 (Suppl 1), 77–79 (2003). https://doi.org/10.1038/ng1204
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DOI: https://doi.org/10.1038/ng1204
