LncDLSM: Identification of Long Non-Coding RNAs With Deep Learning-Based Sequence Model

Long non-coding RNAs (LncRNAs) serve a vital role in regulating gene expressions and other biological processes. Differentiation of lncRNAs from protein-coding transcripts helps researchers dig into the mechanism of lncRNA formation and its downstream regulations related to various diseases. Previous works have been proposed to identify lncRNAs, including traditional bio-sequencing and machine learning approaches. Considering the tedious work of biological characteristic-based feature extraction procedures and inevitable artifacts during bio-sequencing processes, those lncRNA detection methods are not always satisfactory. Hence, in this work, we presented lncDLSM, a deep learning-based framework differentiating lncRNA from other protein-coding transcripts without dependencies on prior biological knowledge. lncDLSM is a helpful tool for identifying lncRNAs compared with other biological feature-based machine learning methods and can be applied to other species by transfer learning achieving satisfactory results. Further experiments showed that different species display distinct boundaries among distributions corresponding to the homology and the specificity among species, respectively.