Research On The Interference Of The MRNA By IncRNA Based On Secondary Structure

The research methods of RNA are mainly divided into two parts: biologicalmethods and calculational methods. In biological means, primarily through a numberof biotechnology, such as using biochips to determine the different expression oflncRNA; using fluorescence-labeled to determine the expression of RNA in aparticular tissue or a cell; using immunoprecipitation to verify the interaction of theRNA and other RNAs or other proteins. Also in some diseases, the researchersanalyze the degree of influence on the disease by making the expression of RNAlower or higher. In computing means, the study are primarily divided into two angles,their own angle and the interactions angle. In their own angle, secondary structure isthe emphasis of the study, because the structure has more conservation than the basicsequence; in the point of the interaction, RNAs usually play an important role byinteracting with other RNAs or proteins, not only through itself. LncRNA hasattracted more and more attention, because of the important role in many biologicalprocesses. In the study of lncRNA, the biological method requires a lot of resources;the accuracy of the secondary struture method is very low because of the length oflncRNA.The main purpose of this paper is to search the most likely lncRNA for themRNA in the set of the mRNA and lncRNA data which were provided by thecooperation unit. Because the study of the binding is very rare, we analysis thecharacteristics of the mRNA’s binding data, and the function method of lncRNA toconstruct the algorithm. we analysis the collected mRNAbinding data in the statisticalangel, and extract the new feature of mRNA—the ratio of the number of theoverlapping bases with the stem and the number of the total bases in the sites of thetargeted mRNA, and conbining the feature with the feature of the stability of the base pair, the content of CG base pairing, the number of continuous base paring toconstruct the scoring model. And we proposed the interference algorithm based on thesecondary structure, and put the scoring model to the algorithm. The first step of thealgorithm is using the dynamic programming method to constructtwo-dimensional matrix for mRNA and lncRNA, and filtering out all the bindingsequence segment of the mRNA-lncRNA binding which meet the requirements; thesecond step is using the scoring model to rate all the binding sequence segment, andsaving the top10scores as the candidate binding sequences; the third step is using therecent energy neighbor model based on the the principle of minimum free energy tocalculate the energy of the candidate binding sequences; the fourth step is usinggreedy algorithm to select the binding sequence which has the higher score and thelower energy; we use the algorithm to screen out the most likely binding sequence ofmRNAand lncRNA, so the lncRNAis the most likely lncRNAto interfer the mRNA.We use the algorithm to search for the lncRNA for all the mRNA that from thecooperation unit, and feedback the result to them. They find75%of the mRNAdisturber by the lncRNAwe predict.