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
  • ASAP (participant of the NAR 06 paper)
  • GenoBase (participant of the NAR 06 paper)
  • EcoCyc (participant of the NAR 06 paper)
  • EcoGene (participant of the NAR 06 paper)
  • RegulonDB (?)
  • KEGG: AA and nucleotide sequences (imported from Genbank)
description

function

localization

process (GO definitions )

gene name (namespace1)

gene name (namespace2)
Some namespaces:

  • genbank ID
  • pdb ID
  • ecogene ID
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 How this is handled in different databases
DNA location Gene name
sequence related sequence (BLAST)

Query by Function

Query inputs and outputs
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

Query inputs and outputs
Input Output How this is handled in different databases
strain ID
  • gene name
  • mutation
  • source
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