In-silico Analysis of LncRNA-mRNA Target Prediction
Long noncoding RNAs (lncRNAs) constitutes a class of noncoding RNAs which are versatile molecules and perform various regulatory functions. Hence, identifying its target mRNAs is an important step in predicting the functions of these molecules. Current lncRNA target prediction tools are not efficient enough to identify lncRNA-mRNA interactions accurately. The reliability of these methods is an issue, as interaction site detections are inaccurate quite often. In this paper our aim is to predict the lncRNA-mRNA interactions efficiently, incorporating the sequence, structure, and energy-based features of the lncRNAs and mRNAs. A brief study on the existing tools for RNA-RNA interaction helped us to understand the different binding sites, and after compiling the tools, we have modified the algorithms to detect the accessible sites and their energies for each interacting RNA sequence. Further RNAstructure tool is used to get the hybrid interaction structure for the accessible lncRNA and mRNA sites. It is found that our target prediction tool gives a better accuracy over the existing tools, after encompassing the sequence, structure, and energy features.
KeywordsLong non-coding RNA Accessible sites RNA structure Target prediction Machine learning
We would like to thank Dr. Zhumur Ghosh (Assistant Professor, Bose Institute) and Sibun Parida (Research Associate, Bioinformatics Center) for their valuable support.
- 1.Available at https://www.lncrnablog.com/what-are-lncrnas/
- 4.Szczeniak, M.W., Makaowska, I.: lncRNA-RNA interactions across the human transcriptome. PloS One 11(3), e0150353 (2016)Google Scholar
- 9.Fukunaga, T., Hamada, M.: RIblast: an ultrafast RNA RNA interaction prediction system based on a seed-and-extension approach. Bioinformatics (2017)Google Scholar
- 11.Hofacker, I.L.: RNA secondary structure analysis using the Vienna RNA package. In: Current Protocols in Bioinformatics, pp. 12–22 (2009)Google Scholar
- 12.Available at https://www.ncbi.nlm.nih.gov/projects/genome
- 13.Kawaguchi, R., Kiryu, H.: Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinfo. 17(1), 203 (2016)Google Scholar
- 17.Available at http://rna.urmc.rochester.edu/RNAstructureWeb