Genome Browsers |
Genome DBs |
EST DBs |
Map DBs |
Sequence Searches
The three major genome browsers are listed below, together with links to detailed information on the annotations at each of the three portals.
- Ensembl
- http://www.ensembl.org.
- Distributed Annotation System
- Ensembl Science Documentation
- NCBI Map Viewer
- http://www.ncbi.nlm.nih.gov/mapview/
- NCBI Contig Assembly and Annotation Process
- UCSC Genome Browser
- http://genome.ucsc.edu
- UCSC Annotation Database
Also see OBC's local GBrowse Installation
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.
- STACK
- http://www.sanbi.ac.za/Dbases.html
- TIGR Gene Indices
- http://www.tigr.org/tdb/tgi.shtml
- UniGene
- http://www.ncbi.nlm.nih.gov/UniGene
The databases listed below represent a significant portion of the data underlying current human genome assemblies. Many of these data are available through GenBank, but each database contains additional information regarding clones, constructs and similar that is not available through the major sequence repositories.
- 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
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- GeneMap '99
- http://www.ncbi.nlm.nih.gov/genemap99
- GenMapDB
- http://genomics.med.upenn.edu/genmapdb
- Généthon linkage map
- http://www.genethon.fr/index_en.html
- HuGeMap
- http://www.infobiogen.fr/services/Hugemap
- Marshfield genetic maps
- http://research.marshfieldclinic.org/genetics/Map_Markers/maps/IndexMapFrames.html
- RHdb
- http://corba.ebi.ac.uk/RHdb
- Stanford G3 and TNG radiation hybrid maps
- http://www-shgc.stanford.edu/RH/
In addition to the databases listed in the section above, there are numerous online resources and databases containing genome-related data. The 'Genome Central' and 'Genome Hub' sites provide jumping-off points to major genome-based web sites. In addition, few representative sitea are also listed below.
- 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
- Cancer Genome Anatomy Project (CGAP)
- http://www.ncbi.nlm.nih.gov/CGAP/
- Genome DataBase (GDB)
- http://www.gdb.org
- HUGO Gene Nomenclature
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- Online Mendelian Inheritance in Man (OMIM)
- http://www.ncbi.nlm.nih.gov/Omim
- SNP Consortium
- http://snp.cshl.org
The lsit below represents 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.
- BLAST
- http://www.ncbi.nlm.nih.gov/BLAST/
- BLAT
- http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
- Ensembl BLAST
- http://www.ensembl.org/Homo_sapiens/blastview
- SSAHA
- http://www.ensembl.org/Homo_sapiens/ssahaview
Steve Mathias smathias at unm dot edu
Last modified: Wed Apr 21 09:20:35 MDT 2004