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EchoBASE

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Link/URL:

EchoBASE

What:

Curated experimental and bioinformatic information about E. coli genes and gene products

Who:
  • Raju Misra
  • Richard Horler
  • Gavin Thomas
Updates:
Upcoming events:
Web Services:


Contents

About EchoBASE

EchoBASE curates experimental and bioinformatic information about E. coli genes and their gene products. The aim of this database is to provide information that will lead to functional predictions for gene products of unknown function. EchoBASE is part of the International E. coli Alliance.

Content

As of July 11, 2006, there are 303 curated references in EchoBASE. The database contains descriptions of papers with information on the function of individual gene products, as well as the actual data from larger, post-genomic studies, which can be searched and manipulated. There are 106 curated experiments which are grouped by type: Biochemistry (10), Bioinformatics (11), Genetics (13), Microarray (6), Protein-Protein Interaction (3), Proteomics (15), Structure (46), and Transcript Level (2).

Other features of EchoBASE are Orphan Enzymes (>90 enzyme activities that have been measured in E. coli, but not mapped to a gene product or gene), EchoABC (a comprehensive list of ABC transporters with links to references and structures, if known), EchoLOCATION (experimentally determined or predicted subcellular location of E. coli products[1]), and EchoPDB (a list of all known structures for E. coli proteins with links to references and the PDB).

Using EchoBASE

Browsing

The curated experimental datasets can be browsed by experiment type.

Searching

EchoBASE can be searched by gene name. The results page for a gene name search contains the ECK no., synonyms, known or predicted function of the gene product, links to the DNA and protein sequences, position on the genome, a map with approx. 5 kb of flanking DNA, links to the gene in other databases, and a list of the experiments where the gene, its transcript, or product was detected with links to the data.

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content

Technology

Web Services/API

Discussion

References

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See Help:References for how to manage references in EcoliWiki.

  1. Horler, RS et al. (2009) EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. Bioinformatics 25 163-6 PubMed EcoliWiki page

Thomas, G.H. (1999) Completing the E. coli proteome: a database of gene products characterised since completion of the genome sequence. Bioinformatics 15:860-861.

Misra, R.V. et al. (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33(Database issue):D329-33

External Links

EchoBASE

Discussion of EchoBASE on other websites