MetaPred2CS: A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins

Altan Kara; Martin Vickers; Martin Swain; David Whitworth; Narcis Fernandez-Fuentes

doi:10.1093/bioinformatics/btw403

MetaPred2CS: A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins

Altan Kara, Martin Vickers, Martin Swain, David Whitworth, Narcis Fernandez-Fuentes

Adran y Gwyddorau Bywyd

Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid

2 Dyfyniadau (Scopus)

91 Wedi eu Llwytho i Lawr (Pure)

Crynodeb

Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.

Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring vs. orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets.

Availability: Web server at: http://metapred2cs.ibers.aber.ac.uk/, Source code: https://github.com/martinjvickers/MetaPred2CS or implemented as Virtual Machine at: http://metapred2cs.ibers.aber.ac.uk/download

Iaith wreiddiol	Saesneg
Tudalennau (o-i)	3339-3341
Nifer y tudalennau	3
Cyfnodolyn	Bioinformatics
Cyfrol	32
Rhif cyhoeddi	21
Dyddiad ar-lein cynnar	04 Gorff 2016
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1093/bioinformatics/btw403
Statws	Cyhoeddwyd - 01 Tach 2016

Mynediad at Ddogfen

10.1093/bioinformatics/btw403

MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteinsLlawysgrif awdur wedi’i dderbyn, 109 KB

Cysylltiad parhaol

Dolen barhaus

Ffeiliau eraill a chysylltiadau

http://hdl.handle.net/2160/43904

Narcis Fernandez Fuentes
- naf4aber.acuk
- Athrofa y Gwyddorau Biolegol, Amgylcheddol a Gwledig - Reader
Unigolyn: Ymchwil
David Whitworth
- dewaber.acuk
- Adran y Gwyddorau Bywyd - Professor
Unigolyn: Dysgu ac Ymchwil

1 Wedi Gorffen

Bioinformatics and genomic and phenomic platform development
Armstead, I. (Prif Ymchwilydd), Boyle, R. (Prif Ymchwilydd), Doonan, J. (Prif Ymchwilydd), Fernandez Fuentes, N. (Prif Ymchwilydd), Gay, A. (Prif Ymchwilydd), Hegarty, M. (Prif Ymchwilydd), Huang, L. (Prif Ymchwilydd), Neal, M. (Prif Ymchwilydd), Swain, M. (Prif Ymchwilydd) & Thomas, I. (Prif Ymchwilydd)
01 Ebr 2012 → 31 Maw 2017
Prosiect: Ymchwil a ariannwyd yn allanol

Dyfynnu hyn

@article{bbbdf0e874ec47e39a2b1a0b1bb4ac74,

title = "MetaPred2CS: A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins",

abstract = "Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring vs. orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets.Availability: Web server at: http://metapred2cs.ibers.aber.ac.uk/, Source code: https://github.com/martinjvickers/MetaPred2CS or implemented as Virtual Machine at: http://metapred2cs.ibers.aber.ac.uk/download",

author = "Altan Kara and Martin Vickers and Martin Swain and David Whitworth and Narcis Fernandez-Fuentes",

note = "This is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/bioinformatics/btw403",

year = "2016",

month = nov,

day = "1",

doi = "10.1093/bioinformatics/btw403",

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T1 - MetaPred2CS

T2 - A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins

AU - Kara, Altan

AU - Vickers, Martin

AU - Swain, Martin

AU - Whitworth, David

AU - Fernandez-Fuentes, Narcis

N1 - This is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/bioinformatics/btw403

PY - 2016/11/1

Y1 - 2016/11/1

N2 - Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring vs. orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets.Availability: Web server at: http://metapred2cs.ibers.aber.ac.uk/, Source code: https://github.com/martinjvickers/MetaPred2CS or implemented as Virtual Machine at: http://metapred2cs.ibers.aber.ac.uk/download

AB - Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring vs. orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets.Availability: Web server at: http://metapred2cs.ibers.aber.ac.uk/, Source code: https://github.com/martinjvickers/MetaPred2CS or implemented as Virtual Machine at: http://metapred2cs.ibers.aber.ac.uk/download

UR - http://hdl.handle.net/2160/43904

U2 - 10.1093/bioinformatics/btw403

DO - 10.1093/bioinformatics/btw403

M3 - Article

C2 - 27378293

SN - 1367-4803

VL - 32

SP - 3339

EP - 3341

JO - Bioinformatics

JF - Bioinformatics

IS - 21

ER -

MetaPred2CS: A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins

Crynodeb

Mynediad at Ddogfen

Cysylltiad parhaol

Ffeiliau eraill a chysylltiadau

Ôl bys

Proffiliau

Narcis Fernandez Fuentes

David Whitworth

Prosiectau

Bioinformatics and genomic and phenomic platform development

Dyfynnu hyn