TERL: classification of transposable elements by convolutional neural networks

Abstract

Transposable elements (TEs) are the most represented sequences occurring in eukaryotic genomes. Few methods provide the classification of these sequences into deeper levels, such as superfamily level, which could provide useful and detailed information about these sequences. Most methods that classify TE sequences use handcrafted features such as k-mers and homology-based search, which could be inefficient for classifying non-homologous sequences. Here we propose an approach, called transposable elements pepresentation learner (TERL), that preprocesses and transforms one-dimensional sequences into two-dimensional space data (i.e., image-like data of the sequences) and apply it to deep convolutional neural networks. This classification method tries to learn the best representation of the input data to classify it correctly. We have conducted six experiments to test the performance of TERL against other methods. Our approach obtained macro mean accuracies and F1-score of 96.4% and 85.8% for superfamilies and 95.7% and 91.5% for the order sequences from RepBase, respectively. We have also obtained macro mean accuracies and F1-score of 95.0% and 70.6% for sequences from seven databases into superfamily level and 89.3% and 73.9% for the order level, respectively. We surpassed accuracy, recall and specificity obtained by other methods on the experiment with the classification of order level sequences from seven databases and surpassed by far the time elapsed of any other method for all experiments. Therefore, TERL can learn how to predict any hierarchical level of the TEs classification system and is about 20 times and three orders of magnitude faster than TEclass and PASTEC, respectively https://github.com/muriloHoracio/TERL. Contact:murilocruz@alunos.utfpr.edu.br.

Keywords: convolutional neural networks; deep learning; representation learning; sequence classification; transposable elements.