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Prediction method and device for RNA false knot structure based on k stems

A technology of ribonucleic acid and prediction method, applied in the field of bioinformatics engineering

Inactive Publication Date: 2015-01-21
SHANDONG JIANZHU UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[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

Method used

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  • Prediction method and device for RNA false knot structure based on k stems
  • Prediction method and device for RNA false knot structure based on k stems
  • Prediction method and device for RNA false knot structure based on k stems

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[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 ).

[0047] Depend on Figure 4 Know: W(1,30)=ES 1 (1,19)+ES 1 (7,30)+W(6,6)+W(13,14)+W(20,24)

Embodiment 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 invention provides a prediction method and device for an RNA false knot structure based on k stems. The prediction method comprises the following steps that a section of RNA base sequence is input, and false knots and k (k is larger than or equal to one) stems are defined; RNA bases and k stems are searched for from left to right, and all the found k stems are subjected to determined marking; the false knots are searched for according to the characteristic that the k stems intersect to form the false knots, and the minimum free energy of the RNA false knot structure including the k stems is calculated; the RNA false knot structure is output. According to the prediction method, the searching speed is high, the accuracy is high, and the sensibility, specificity and the like are better than that of other related algorithms such as a PKNOTS algorithm. The prediction method is more effective on the aspect of plane false knot prediction than the PKNOTS algorithm.

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...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
Inventor 刘振栋马宏伟倪明琨李恒武赵世民杨朝晖于庆华高贻明
Owner SHANDONG JIANZHU UNIV
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