Method and device for predicting ribonucleic acid pseudoknot structure based on k-stem
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A technology of ribonucleic acid and prediction method, applied in the field of bioinformatics engineering
Inactive Publication Date: 2017-10-20
SHANDONG JIANZHU UNIV +1
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[0006] The technical problem solved by the present invention is to reduce the time complexity and space complexity of prediction and improve the accuracy of prediction for RNA structure prediction, especially for the prediction method of RNA structure based on k-stem containing pseudoknot
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[0042] In RNA pseudoknot structure prediction, if k=1 or k=2 in k stems, the program calculations related to 1 stem and 2 stems are as follows.
[0043] Procedure 1: Calculation of energy and length for 1 stem and 2 stem
[0044]
[0045]
[0046] Figure 4 Give a simple false knot. Use two 1 stem (S 1 [1,19], S 1 [7,30]) and three subsequences (s 6,6 , s 13,14 , s 20,24 ) form a false knot. Since each 1-stem is determined by two parameters, the storage of 1-stem requires O(n 2 ) space, so the time complexity of calculating the false knot is O(n 4 ), the space complexity is O(n 2 ).
[0049] Given a sequence s=s 1 the s 2 …s n , the sequence fragment s i,j =s i …s j , 1i,j The corresponding minimum energy of the secondary structure S containing pseudoknots. Let V(i,j) be s i and s j In the case of constituting a base pair (i,j), the subsequence S i,j The corresponding minimum energy of the secondary structure S containing pseudoknots.
[0050] Figure 5 Give the calculation schema of W(i,j) and V(i,j). W(i,j) containing pseudoknot structure is calculated by the following 4 cases:
[0051] 1)s j is an unpaired base, base s i and s j-1 The pairing relationship is not determined, such as Figure 5 .1, calculated W(i,j)=W(i,j-1);
[0052] 2)s i is an unpaired base, base s i+1 and s j The pairing relationship is not determined, such as Figure 5 .2, Calculated W(i,j)=W(i+1,j);
[0053] 3)s i and s k ,s k+1 and s j do not constitute a base pair and are in different subsequences S i,k and S k+1,j In the corresponding secondary structure, ...
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Abstract
The present invention provides a kind of prediction method and device of the ribonucleic acid (RNA) pseudoknot structure based on k stem, and prediction method comprises the following steps: input a section of ribonucleic acid base sequence; Define pseudoknot, k (k≥1) stem; From Search RNA bases and k stems from left to right, and mark all k stems found out; according to the characteristics of k stems crossing to form pseudoknots, find pseudoknots; calculate the minimum structure of ribonucleic acid pseudoknots containing k stems Free energy; pseudoknot structure for export of ribonucleic acid. The method involved in the present invention has fast search speed, high correct rate, sensitivity and specificity, and is superior to other related algorithms, such as PKNOTS algorithm. This method is more effective than the PKNOTS algorithm in the prediction of planar pseudoknots.
Description
technical field [0001] The invention belongs to the field of biological information engineering and relates to a method for predicting the pseudoknot structure of ribonucleic acid (hereinafter referred to as RNA), in particular to a method and a device for predicting the pseudoknot structure of RNA based on k-stem. Background technique [0002] RNA is one of the most important macromolecules in biological systems. It performs multiple functions in organisms and is a template for protein synthesis. RNA secondary structure prediction is used for protein function analysis and is the basis for RNA tertiary structure prediction. Pseudoknot is the most extensive structural unit in RNA, and it is a very complex and stable RNA structure. Pseudoknot has structural, catalytic and regulatory functions in RNA molecules, and is the key point in the current research on RNA structure prediction. [0003] There are two main methods for RNA secondary structure prediction: the early method i...
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