A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts

Hugo W. Schneider, Taina Raiol, Marcelo M. Brigido, Maria Emilia M. T. Walter, Peter F. Stadler

In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts. The proposed method is based on SVM and uses the first ORF relative length and frequencies of nucleotide patterns selected by PCA as features. FASTA files were used as input to calculate all possible features. These features were divided in two sets: (i) 336 frequencies of nucleotide patterns; and (ii) 4 features derived from ORFs. PCA were applied to the first set to identify 6 groups of frequencies that could most contribute to the distinction. Twenty-four experiments using the 6 groups from the first set and the features from the second set where built to create the best model to distinguish lncRNAs from PCTs. This method was trained and tested with human (Homo sapiens), mouse (Mus musculus) and zebrafish (Danio rerio) data, achieving 98.21%, 98.03% and 96.09%, accuracy, respectively. Our method was compared to other tools available in the literature (CPAT, CPC, iSeeRNA, lncRNApred, lncRScan-SVM and FEELnc), and showed an improvement in accuracy by ≈3.00%. In addition, to validate our model, the mouse data was classified with the human model, and vice-versa, achieving ≈97.80% accuracy in both cases, showing that the model is not overfit. The SVM models were validated with data from rat (Rattus norvegicus), pig (Sus scrofa) and fruit fly (Drosophila melanogaster), and obtained more than 84.00% accuracy in all these organisms. Our results also showed that 81.2% of human pseudogenes and 91.7% of mouse pseudogenes were classified as non-coding. Moreover, our method was capable of re-annotating two uncharacterized sequences of Swiss-Prot database with high probability of being lncRNAs. Finally, in order to use the method to annotate transcripts derived from RNA-seq, previously identified lncRNAs of human, gorilla (Gorilla gorilla) and rhesus macaque (Macaca mulatta) were analyzed, having successfully classified 98.62%, 80.8% and 91.9%, respectively. The SVM method proposed in this work presents high performance to distinguish lncRNAs from PCTs, as shown in the results. To build the model, besides using features known in the literature regarding ORFs, we used PCA to identify features among nucleotide pattern frequencies that contribute the most in distinguishing lncRNAs from PCTs, in reference data sets. Interestingly, models created with two evolutionary distant species could distinguish lncRNAs of even more distant species.