Method and device for predicting ribonucleic acid folding structure based on extended structure with pseudoknots

Abstract

The invention provides a method and a device for predicting a ribonucleic acid folding structure containing a pseudoknot based on an extended structure. The method comprises the following steps of randomly inputting one segment of a ribonucleic acid base sequence, defining a pseudoknot and the extended structure, establishing a ribonucleic acid pseudoknot structure characteristic model and a mathematical structure which comprise the pseudoknot and the extended structure, calculating lowest base free energy of the characteristic model, and outputting the ribonucleic acid folding structure whichcomprises the pseudoknot. The device comprises an input unit, an initializing unit, a storage unit, a calculating unit and an output unit. The method and the device realize calculation based on the extended structure. Furthermore continuous stacking and coaxial staking based on the extended structure are introduced, thereby forming an integral and accurate RNA folding structure which comprises the continuous stack, the extended structure, an annular structure and a pseudoknot structure. The searching speed, the accuracy, the sensitivity and the singularity are obviously better than that of prior art. Furthermore the method and the device realize higher effectiveness in predicting the planar pseudoknot and a non-planar pseudoknot structure.

Description

technical field [0001] The invention relates to a method for predicting the pseudoknot structure and extended structure of ribonucleic acid (hereinafter referred to as RNA), in particular to a method and device for predicting the folded structure of ribonucleic acid based on the extended structure including pseudoknot, and belongs to the field of bioinformatics engineering . Background technique [0002] Ribonucleic acid (abbreviated as RNA, that is, Ribonucleic Acid), RNA is a single strand formed by transcription based on a strand of DNA as a template and based on the principle of complementary base pairing. It exists in biological cells and some viruses and viroids. information carrier. RNA is a long chain molecule formed by condensation of ribonucleotides through phosphodiester bonds. A ribonucleotide molecule consists of phosphate, ribose sugar and bases. There are four main bases in RNA, namely A adenine, G guanine, C cytosine, and U uracil. The main function is to...

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Problems solved by technology

[0009] Although the above method is more effective than the PKNOTS algorithm in predicting the pseudoknot structure, the representation model of the pseudoknot has defects such as low parameter accuracy, inaccurate free energy values, and large calculation errors, which make it difficult to predict the pseudoknot structure. The search speed, correct rate, sensitivity and specificity have not yet achieved the ideal effect and need to be further improved

[0010] Therefore, it is necessary to propose the concept of extended structure, and the two ribonucleic acid sequence fragments s i,k and s l,j The internal and external base pairing rules in the paper are specified to make it closer to the real structure, so as to solve the defects of low parameter accuracy, inaccurate free energy value, and large calculation method error in the prediction of RNA folding structure including false knots, so that Significantly improved search speed, correct rate, sensitivity and specificity

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