AccessE-Algorithm to detect the accessible segments during LncRNA-mRNA interactions

Long noncoding RNAs (lncRNAs) constitutes a class of noncoding RNAs which are versatile molecules and perform various regulatory functions. A significant number of lncRNAs have been found in different organisms including Homo sapiens, but their functions are yet to be explored fully. LncRNAs target protein coding genes or mRNAs to regulate different functions. Hence it is highly challenging to find out its key target molecule and understand the function of these molecules. Predicting accessible energy between an lncRNA and an mRNA is an essential step to identify lncRNA targets further. The existing algorithms used for accessible energy calculation has several limitations and are unable to predict comprehensive interaction between lncRNAs and mRNAs. We have developed AccessE which identifies accessible segments of lncRNA and mRNA and provides the accessible energy of the two molecules. AccessE has been used to calculate the accessible energy for a set of experimentally validated lncRNA-target mRNA pairs. Proper evaluation of accessible energy between multiple accessible segments of lncRNA and mRNA, provides in-depth understanding of lncRNA-mRNA interaction.