Database Overview: Difference between revisions
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==Query by DNA location== | ==Query by DNA location or sequence== | ||
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|+ '''Query inputs and outputs''' | |+ '''Query inputs and outputs''' | ||
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|DNA location | |DNA location | ||
|Gene name | |Gene name | ||
| [[ASAP]] (replace these) | |||
| [[GenoBase]] | |||
| [[EcoCyc]] | |||
| [[EcoGene]] | |||
| [[RegulonDB]] | |||
| Other | |||
| Notes | |||
|- | |||
|sequence | |||
|related sequence (BLAST) | |||
| [[ASAP]] (replace these) | | [[ASAP]] (replace these) | ||
| [[GenoBase]] | | [[GenoBase]] | ||
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| Notes | | Notes | ||
|} | |} | ||
==Query by Function== | ==Query by Function== | ||
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Revision as of 16:36, 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 (namespace1) |
gene name (namespace2) | |||||||
|
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 |
| 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 |
Query by DNA location or sequence
| Input | Output | ASAP | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
|---|---|---|---|---|---|---|---|---|
| DNA location | Gene name | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
| sequence | related sequence (BLAST) | ASAP (replace these) | GenoBase | EcoCyc | EcoGene | RegulonDB | Other | Notes |
Query by Function
| Input | Output | ASAP | 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 |
| 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 |