Database Overview: Difference between revisions
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| Line 17: | Line 17: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: AA and nucleotide sequences | |||
|- | |- | ||
|description<BR> | |description<BR> | ||
| Line 25: | Line 26: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: text definition / functional description | |||
|- | |- | ||
| | | | ||
| Line 34: | Line 36: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| rowspan ='4'| | | rowspan ='4'| | ||
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*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| | | | ||
| Line 58: | Line 62: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| | | | ||
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*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
|gene name | |gene name | ||
| Line 76: | Line 82: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry | |||
|- | |- | ||
| rowspan='3'|gene name | | rowspan='3'|gene name | ||
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*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| | | | ||
| Line 97: | Line 105: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
|gene name (species 1) | |gene name (species 1) | ||
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*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes | |||
|- | |- | ||
| Line 117: | Line 127: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| | | | ||
| Line 126: | Line 137: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|- | |- | ||
| | | | ||
| Line 135: | Line 147: | ||
*[[EcoGene]] | *[[EcoGene]] | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | |||
|} | |} | ||
Revision as of 15:32, 21 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 |
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| metabolic process |
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Query by DNA location or sequence
| Input | Output | How this is handled in different databases |
|---|---|---|
| DNA location | Gene name | |
| sequence | related sequence (BLAST) |
Query by Function
| Input | Output | How this is handled in different databases |
|---|---|---|
| gene function (GO term) same for process and other GO branches |
gene name |
Query by strain
| Input | Output | How this is handled in different databases |
|---|---|---|
| strain ID |
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