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Open Access Short Report

Machine learning on normalized protein sequences

Dominik Heider1*, Jens Verheyen2 and Daniel Hoffmann1

Author Affiliations

1 Department of Bioinformatics, Center of Medical Biotechnology, University of Duisburg-Essen, Universitaetsstr. 2, 45117 Essen, Germany

2 Institute of Virology, University of Cologne, Fuerst-Pueckler-Str. 56, 50935 Cologne, Germany

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BMC Research Notes 2011, 4:94  doi:10.1186/1756-0500-4-94

Published: 31 March 2011

Abstract

Background

Machine learning techniques have been widely applied to biological sequences, e.g. to predict drug resistance in HIV-1 from sequences of drug target proteins and protein functional classes. As deletions and insertions are frequent in biological sequences, a major limitation of current methods is the inability to handle varying sequence lengths.

Findings

We propose to normalize sequences to uniform length. To this end, we tested one linear and four different non-linear interpolation methods for the normalization of sequence lengths of 19 classification datasets. Classification tasks included prediction of HIV-1 drug resistance from drug target sequences and sequence-based prediction of protein function. We applied random forests to the classification of sequences into "positive" and "negative" samples. Statistical tests showed that the linear interpolation outperforms the non-linear interpolation methods in most of the analyzed datasets, while in a few cases non-linear methods had a small but significant advantage. Compared to other published methods, our prediction scheme leads to an improvement in prediction accuracy by up to 14%.

Conclusions

We found that machine learning on sequences normalized by simple linear interpolation gave better or at least competitive results compared to state-of-the-art procedures, and thus, is a promising alternative to existing methods, especially for protein sequences of variable length.