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EcoGene, comprehensive data resource for E. coli
Kenn Rudd, Univ. of Miami Med School
EcoGene is a manually curated resource containing genomic and proteomic information about E.coli K-12 MG1655. EcoGene works with the CGSC to manage the assignment of canonical gene names for E. coli genes.
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.
|Title, author, or reference ID||Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links|
|Enzyme(s) and Genomic Adress||Restriction Map|
- Find the neighboring genes to the initially identified set
Yes. EcoMap (10 kb neighboring genes)
- Find/design primers for a certain gene
- Find all the clones/KOs for those genes
Yes. Link to CGSC and GenoBase
- Find commonalities in function in the genes that are up or down-regulated in a given experiment
- Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)
- Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)
- For a gene, segment of DNA, operon/regulons, pathway , find all the available information
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- Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 28 60-4 PubMed