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Bioinformatics Advance Access originally published online on November 16, 2008
Bioinformatics 2009 25(2):163-166; doi:10.1093/bioinformatics/btn596
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations

Richard S. P. Horler 1, Andrew Butcher 1, Nikitas Papangelopoulos 1, Peter D. Ashton 2 and Gavin H. Thomas 1,*

1Department of Biology (Area 10) and 2Technology Facility, Department of Biology, University of York, PO BOX 373, York YO10 5YW, UK

*To whom correspondence should be addressed.


  Abstract

Summary: EchoLOCATION is a database that provides a comprehensive analysis of the subcellular locations of Escherichia coli K-12 proteins. Locations are predicted by integrating data from a range of publicly available algorithms combined with extensive curation of experimental literature. The data can be searched in a variety of ways and can generate lists of subcellular proteomes for analysis. Experimental evidence supports the locations of over 500 envelope proteins (periplasm, inner and outer membrane). From analysis of disagreements between in silico predictions and experimental data, we provide an analysis of protein types where subcellular prediction algorithms are currently not accurate.

Availability: http://www.ecoli-york.org/

Contact: ght2{at}york.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on May 20, 2008; revised on October 20, 2008; accepted on November 13, 2008

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