Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

Method and device for predicting ribonucleic acid pseudoknot structure based on k-stem

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
View PDF2 Cites 0 Cited by
  • 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

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method and device for predicting ribonucleic acid pseudoknot structure based on k-stem
  • Method and device for predicting ribonucleic acid pseudoknot structure based on k-stem
  • Method and device for predicting ribonucleic acid pseudoknot structure based on k-stem

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, ...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

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...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/22
Inventor 刘振栋马宏伟叶红朝赵世民倪明琨刘芳含江凯李恒武孙庆霞杨朝晖于庆华高贻明
Owner SHANDONG JIANZHU UNIV
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com