Database Overview: Difference between revisions
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| Line 14: | Line 14: | ||
| Notes | | Notes | ||
|- | |- | ||
|gene name (e.g. lacY) sequence | | rowspan = '2'|gene name (e.g. lacY) sequence | ||
|description<BR> | |description<BR> | ||
| [[ASAP]] | |||
| [[GenoBase]] | |||
| [[EcoCyc]] | |||
| [[EcoGene]] | |||
| [[RegulonDB]] | |||
| Other | |||
| Notes | |||
|- | |||
| | |||
function,localization,process (GO definitions )<BR> | function,localization,process (GO definitions )<BR> | ||
| [[ASAP]] | | [[ASAP]] | ||
| [[GenoBase]] | | [[GenoBase]] | ||
| [[EcoCyc]] | | [[EcoCyc]] | ||
| Line 25: | Line 34: | ||
| Notes | | Notes | ||
|- | |- | ||
|gene name (genbank namespace)<BR> | | rowspan ='4'|gene name (genbank namespace)<BR> | ||
more generally<BR> | more generally<BR> | ||
gene name (namespace1) | gene name (namespace1) | ||
| Line 32: | Line 41: | ||
gene name (namespace2)<BR> | gene name (namespace2)<BR> | ||
Some namespaces: | Some namespaces: | ||
|- | |||
| | |||
*genbank | *genbank | ||
| [[ASAP]] | |||
| [[GenoBase]] | |||
| [[EcoCyc]] | |||
| [[EcoGene]] | |||
| [[RegulonDB]] | |||
| Other | |||
| Notes | |||
|- | |||
| | |||
*pdb | *pdb | ||
| [[ASAP]] (replace these) | |||
| [[GenoBase]] | |||
| [[EcoCyc]] | |||
| [[EcoGene]] | |||
| [[RegulonDB]] | |||
| Other | |||
| Notes | |||
|- | |||
| | |||
*ecogene | *ecogene | ||
| [[ASAP]] (replace these) | | [[ASAP]] (replace these) | ||
| Line 45: | Line 74: | ||
|gene name | |gene name | ||
|pathway | |pathway | ||
| [[ASAP]] | | [[ASAP]] | ||
| [[GenoBase]] | | [[GenoBase]] | ||
| [[EcoCyc]] | | [[EcoCyc]] | ||
| Line 53: | Line 82: | ||
| Notes | | Notes | ||
|} | |} | ||
==Query by pathway== | ==Query by pathway== | ||
{| border="1" align="TOP" | {| border="1" align="TOP" | ||
Revision as of 16:27, 19 June 2006
Features at different databases
Query types
Query by gene name
| Input | Output | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|---|---|---|---|---|---|---|---|---|
| gene name (e.g. lacY) sequence | description |
ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|
function,localization,process (GO definitions ) |
ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
| gene name (genbank namespace) more generally |
gene name (ecogene namespace) more generally | |||||||
|
ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
|
ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
|
ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
| gene name | pathway | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
Query by pathway
| Input | Output | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|---|---|---|---|---|---|---|---|---|
| pathway | gene name | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
Query by DNA location
| Input | Output | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|---|---|---|---|---|---|---|---|---|
| DNA location | Gene name | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| gene function (GO term) same for process and other GO branches |
gene name | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| gene name | experimental data
*gene expression *protein interaction |
ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| sequence | related sequence (BLAST) | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| gene name (species 1) | gene name( species 2) | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| gene name | *mutations
|
ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
Query by strain
| Input | Output | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|---|---|---|---|---|---|---|---|---|
| strain ID | *gene name | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| *mutation | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
| *source | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes | |
| metabolic process | *regulatory circuits | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| *transcription factors/sites | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |