Database Overview

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Content & Features at different databases

Query types

Query by gene name

Query inputs and outputs
Input Output How this is handled in different databases
gene name (e.g. lacY) sequence
description

function,localization,process (GO definitions )

gene name (namespace1)

gene name (namespace2)
Some namespaces:

  • genbank
  • pdb
  • ecogene
gene name pathway
gene name experimental data
  • gene expression
  • protein interaction
gene name (species 1) gene name( species 2)
gene name
  • mutations
  • sequence difference
  • phenotype

Query by pathway

Query inputs and outputs
Input Output How this is handled in different databases
pathway
  • gene name
metabolic process
  • regulatory circuits
  • transcription factors/sites

Query by DNA location or sequence

Query inputs and outputs
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

Query inputs and outputs
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

Query inputs and outputs
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
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