Database Overview: Difference between revisions
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|pathway | |pathway | ||
|gene name | | | ||
*gene name | |||
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*[[ASAP]] | *[[ASAP]] | ||
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| rowspan ='2' |metabolic process | | rowspan ='2' |metabolic process | ||
|*regulatory circuits | | | ||
*regulatory circuits | |||
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*[[ASAP]] | *[[ASAP]] | ||
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*[[RegulonDB]] | *[[RegulonDB]] | ||
|- | |- | ||
|*transcription factors/sites | | | ||
*transcription factors/sites | |||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
Revision as of 22:17, 19 June 2006
Content & Features at different databases
Query types
Query by gene name
| Input | Output | How this is handled in different databases |
|---|---|---|
| gene name (e.g. lacY) | sequence | |
| description |
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function,localization,process (GO definitions ) |
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gene name (namespace1) |
gene name (namespace2) | |
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| gene name | pathway | |
| gene name | experimental data | |
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| gene name (species 1) | gene name( species 2) | |
| gene name |
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Query by pathway
| Input | Output | How this is handled in different databases |
|---|---|---|
| pathway |
|
|
| metabolic process |
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|
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 |
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 |