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Large Scale Identification and Categorization of Protein Sequences Using Structured Logistic Regression

Author

Listed:
  • Bjørn P Pedersen
  • Georgiana Ifrim
  • Poul Liboriussen
  • Kristian B Axelsen
  • Michael G Palmgren
  • Poul Nissen
  • Carsten Wiuf
  • Christian N S Pedersen

Abstract

Background: 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. Results: 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. Conclusions: 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.

Suggested Citation

  • Bjørn P Pedersen & Georgiana Ifrim & Poul Liboriussen & Kristian B Axelsen & Michael G Palmgren & Poul Nissen & Carsten Wiuf & Christian N S Pedersen, 2014. "Large Scale Identification and Categorization of Protein Sequences Using Structured Logistic Regression," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-11, January.
    • Handle: RePEc:plo:pone00:0085139
    DOI: 10.1371/journal.pone.0085139
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    References listed on IDEAS

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    1. Bjørn P. Pedersen & Morten J. Buch-Pedersen & J. Preben Morth & Michael G. Palmgren & Poul Nissen, 2007. "Crystal structure of the plasma membrane proton pump," Nature, Nature, vol. 450(7172), pages 1111-1114, December.
    2. Claus Olesen & Martin Picard & Anne-Marie Lund Winther & Claus Gyrup & J. Preben Morth & Claus Oxvig & Jesper Vuust Møller & Poul Nissen, 2007. "The structural basis of calcium transport by the calcium pump," Nature, Nature, vol. 450(7172), pages 1036-1042, December.
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