Database Overview: Difference between revisions
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| Line 85: | Line 85: | ||
|+ '''Query inputs and outputs''' | |+ '''Query inputs and outputs''' | ||
! '''Input''' !! '''Output''' | ! '''Input''' !! '''Output''' | ||
| [[ASAP]] | | '''[[ASAP]]''' | ||
| [[GenoBase]] | | '''[[GenoBase]]''' | ||
| [[EcoCyc]] | | '''[[EcoCyc]]''' | ||
| [[EcoGene]] | | '''[[EcoGene]]''' | ||
| [[RegulonDB]] | | '''[[RegulonDB]]''' | ||
| Other | | '''Other''' | ||
| Notes | | '''Notes''' | ||
|- | |- | ||
|pathway | |pathway | ||
| Line 123: | Line 123: | ||
|} | |} | ||
==Query by DNA location== | ==Query by DNA location== | ||
{| border="1" align="TOP" | {| border="1" align="TOP" | ||
Revision as of 16:32, 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
| 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 |