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

Richard S. P. Horler; Andrew Butcher; Nikitas Papangelopoulos; Peter D. Ashton; Gavin H. Thomas

doi:10.1093/bioinformatics/btn596

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

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

Biology

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	163-166
Number of pages	4
Journal	Bioinformatics
Volume	25
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/btn596
Publication status	Published - 15 Jan 2009

Keywords

GRAM-NEGATIVE BACTERIA
OUTER-MEMBRANE
SIGNAL PEPTIDES
GENOME SEQUENCE
PREDICTION
IDENTIFICATION
K-12
TOPOLOGY
LIPOPOLYSACCHARIDE
TRANSPORTER

Access to Document

10.1093/bioinformatics/btn596

Cite this

@article{c75f5290e7e54a2c862d38e9a7afcb32,

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

abstract = "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.",

keywords = "GRAM-NEGATIVE BACTERIA, OUTER-MEMBRANE, SIGNAL PEPTIDES, GENOME SEQUENCE, PREDICTION, IDENTIFICATION, K-12, TOPOLOGY, LIPOPOLYSACCHARIDE, TRANSPORTER",

author = "Horler, {Richard S. P.} and Andrew Butcher and Nikitas Papangelopoulos and Ashton, {Peter D.} and Thomas, {Gavin H.}",

year = "2009",

month = jan,

day = "15",

doi = "10.1093/bioinformatics/btn596",

language = "English",

volume = "25",

pages = "163--166",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "2",

}

TY - JOUR

T1 - EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations

AU - Horler, Richard S. P.

AU - Butcher, Andrew

AU - Papangelopoulos, Nikitas

AU - Ashton, Peter D.

AU - Thomas, Gavin H.

PY - 2009/1/15

Y1 - 2009/1/15

N2 - 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.

AB - 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.

KW - GRAM-NEGATIVE BACTERIA

KW - OUTER-MEMBRANE

KW - SIGNAL PEPTIDES

KW - GENOME SEQUENCE

KW - PREDICTION

KW - IDENTIFICATION

KW - K-12

KW - TOPOLOGY

KW - LIPOPOLYSACCHARIDE

KW - TRANSPORTER

UR - http://www.scopus.com/inward/record.url?scp=58349122286&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btn596

DO - 10.1093/bioinformatics/btn596

M3 - Article

SN - 1367-4803

VL - 25

SP - 163

EP - 166

JO - Bioinformatics

JF - Bioinformatics

IS - 2

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Cite this