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

Gwyddorau Bywyd

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

71 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
- Cyfadran Gwyddorau Daear a Bywyd, Athrofa y Gwyddorau Biolegol, Amgylcheddol a Gwledig - Reader
Unigolyn: Dysgu ac Ymchwil
David Whitworth
- dewaber.acuk
- Cyfadran Gwyddorau Daear a Bywyd, Gwyddorau Bywyd - Professor
Unigolyn: Dysgu ac Ymchwil

1 Wedi Gorffen

Bioinformatics and genomic and phenomic platform development
Armstead, I., Boyle, R., Doonan, J., Fernandez Fuentes, N., Gay, A., Hegarty, M., Huang, L., Neal, M., Swain, M. & Thomas, I.
Biotechnology and Biological Sciences Research Council
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