Large scale identification and categorization of protein sequences using structured logistic regression.

<h4>Background</h4>Structured Logistic Regression (SLR) is a newly developed machine learning tool first proposed in the context of text categorization. Current availability of extensive protein sequence databases calls for an automated method to reliably classify sequences and SLR seems...

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Autores principales:	Bjørn P Pedersen, Georgiana Ifrim, Poul Liboriussen, Kristian B Axelsen, Michael G Palmgren, Poul Nissen, Carsten Wiuf, Christian N S Pedersen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1ca32674a916416281ef7f72a391c25f
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spelling	oai:doaj.org-article:1ca32674a916416281ef7f72a391c25f2021-11-18T08:37:19ZLarge scale identification and categorization of protein sequences using structured logistic regression.1932-620310.1371/journal.pone.0085139https://doaj.org/article/1ca32674a916416281ef7f72a391c25f2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24465495/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Structured Logistic Regression (SLR) is a newly developed machine learning tool first proposed in the context of text categorization. Current availability of extensive protein sequence databases calls for an automated method to reliably classify sequences and SLR seems well-suited for this task. The classification of P-type ATPases, a large family of ATP-driven membrane pumps transporting essential cations, was selected as a test-case that would generate important biological information as well as provide a proof-of-concept for the application of SLR to a large scale bioinformatics problem.<h4>Results</h4>Using SLR, we have built classifiers to identify and automatically categorize P-type ATPases into one of 11 pre-defined classes. The SLR-classifiers are compared to a Hidden Markov Model approach and shown to be highly accurate and scalable. Representing the bulk of currently known sequences, we analysed 9.3 million sequences in the UniProtKB and attempted to classify a large number of P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases.<h4>Conclusions</h4>Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.Bjørn P PedersenGeorgiana IfrimPoul LiboriussenKristian B AxelsenMichael G PalmgrenPoul NissenCarsten WiufChristian N S PedersenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e85139 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bjørn P Pedersen Georgiana Ifrim Poul Liboriussen Kristian B Axelsen Michael G Palmgren Poul Nissen Carsten Wiuf Christian N S Pedersen Large scale identification and categorization of protein sequences using structured logistic regression.
description	<h4>Background</h4>Structured Logistic Regression (SLR) is a newly developed machine learning tool first proposed in the context of text categorization. Current availability of extensive protein sequence databases calls for an automated method to reliably classify sequences and SLR seems well-suited for this task. The classification of P-type ATPases, a large family of ATP-driven membrane pumps transporting essential cations, was selected as a test-case that would generate important biological information as well as provide a proof-of-concept for the application of SLR to a large scale bioinformatics problem.<h4>Results</h4>Using SLR, we have built classifiers to identify and automatically categorize P-type ATPases into one of 11 pre-defined classes. The SLR-classifiers are compared to a Hidden Markov Model approach and shown to be highly accurate and scalable. Representing the bulk of currently known sequences, we analysed 9.3 million sequences in the UniProtKB and attempted to classify a large number of P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases.<h4>Conclusions</h4>Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.
format	article
author	Bjørn P Pedersen Georgiana Ifrim Poul Liboriussen Kristian B Axelsen Michael G Palmgren Poul Nissen Carsten Wiuf Christian N S Pedersen
author_facet	Bjørn P Pedersen Georgiana Ifrim Poul Liboriussen Kristian B Axelsen Michael G Palmgren Poul Nissen Carsten Wiuf Christian N S Pedersen
author_sort	Bjørn P Pedersen
title	Large scale identification and categorization of protein sequences using structured logistic regression.
title_short	Large scale identification and categorization of protein sequences using structured logistic regression.
title_full	Large scale identification and categorization of protein sequences using structured logistic regression.
title_fullStr	Large scale identification and categorization of protein sequences using structured logistic regression.
title_full_unstemmed	Large scale identification and categorization of protein sequences using structured logistic regression.
title_sort	large scale identification and categorization of protein sequences using structured logistic regression.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/1ca32674a916416281ef7f72a391c25f
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Large scale identification and categorization of protein sequences using structured logistic regression.

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