Machine learning on normalized protein sequences

Heider, Dominik LSF; Verheyen, Jens LSF; Hoffmann, Daniel LSF

Background <br> 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. <br> <br> Findings <br> 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%. <br> <br> Conclusions <br> 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.


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Heider, D., Verheyen, J., Hoffmann, D., 2011. Machine learning on normalized protein sequences.
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