The list of Web sites listed in Table 11.1 provides a starting point for accessing genomic databases and Web sites. These sites have relatively stable and simple Web addresses that can be typed into the browser window. If this does not work, a Web search for the site will usually work. Each year in January, the journal Nucleic Acids Research publishes a special database issue. This issue is a valuable resource for finding currently available databases of genomic information. Following is a list of Web search terms that may be used to reach additional sites.
Alfresco |
Visualization tool for genomes. |
allgenes.org |
A comprehensive gene index. |
ASD |
Alternative splicing database project. |
CGAP |
Cancer genome anatomy project. |
|
DOGS |
Database of genome sizes. |
E-CELL |
A modeling and simulation environment for cells. |
Ecocyc |
Electronic encyclopedia of E. coli genes. |
Ensembl e! |
Genome browser. |
EpoDBis |
A database of genes that relate to vertebrate red blood cells. |
FAST_PAN |
Automatic searches of online EST databases. |
Flybase |
D. melanogaster: genomic database. |
GAIA |
Genome Annotation and Information. |
GeneCensus |
Genome Comparisons, M. Gerstein laboratory. |
GeneDB |
Parasite genome database. |
Gene Ontology |
System for describing gene functions. |
GeneQuiz |
Integrated system for sequence analysis and management. |
GeneRAGE |
Sequence clustering and domain detection. |
Genew |
Human gene nomenclature database. |
GenProtEC |
E. coli genome and proteome database. |
GFF |
Specifications for describing genes. |
GKB |
Genome knowledgebase of biological processes. |
Golden Path |
Human genome browser. |
Gramene |
Grass genome database. |
IMGT |
ImMunoGeneTics Database. |
KEGG |
Kyoto Encyclopedia of Genes and Genomes. |
MAGPIE |
Genome Project Investigation Environment. |
MaizGDB |
Maize (corn) genomic database. |
MBGB |
Microbial genome database. |
MitBASE, MitoMap |
Mitochondrial Database. |
PEDANT |
A protein extraction, description, and analysis tool. |
RGD, RatMap |
Rat genomic databases. |
RIO |
Automated method for phylogenomic analysis |
RSDB |
Repetitive sequence database. |
SEQUEST |
Identification of proteins following mass spectrometry. |
SGD |
Yeast genomic database. |
SNP consortium |
Collection of SNPs in the human genome. |
STRING |
Search Tool for Neighboring Genes. |
SWISS-2DPAGE |
Two-dimensional polyacrylamide gel electrophoresis database. |
TAIR |
A. thaliana information resource. |
TAMBIS |
Resource for biological information. |
TIGR |
Genome resource especially for prokaryotes. |
WormBase |
C. elegans database. |