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Component-based identification method and device of long-chain RNA secondary structures with pseudo knots

A secondary structure, component-based technology, applied in instrumentation, computing, electrical digital data processing, etc., can solve the problems of neglecting the importance and the inability of computing power to meet the length requirements of RNA structure and function, so as to improve the complexity of space and time and improve recognition The effect of precision

Inactive Publication Date: 2014-02-19
JILIN UNIV
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Problems solved by technology

The common problem with computer identification algorithms that identify the secondary structure of the entire RNA sequence is that current secondary structure identification software is limited to focusing on the accuracy of the global structure, ignoring the functional components that have biological functions and conserved local structures in long-chain RNAs. Importance, especially for the identification of secondary structures containing pseudoknots, and the computing power of existing secondary structure identification software cannot meet the length requirements of RNA structure functions

Method used

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  • Component-based identification method and device of long-chain RNA secondary structures with pseudo knots
  • Component-based identification method and device of long-chain RNA secondary structures with pseudo knots
  • Component-based identification method and device of long-chain RNA secondary structures with pseudo knots

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Embodiment 1

[0036] like figure 1 As shown, the hardware structure diagram of the connection between the component-based long-chain RNA secondary structure recognition device with pseudoknot and the host computer of the present invention includes the RNA secondary structure recognition device composed of the host computer 01 and the ARM9 microprocessor 02.

[0037] In the embodiment of the present invention, generally utilize a general-purpose PC computer as upper computer 01, this upper computer can pass through RS-232 serial port and the RNA secondary structure of the microprocessor based on the 32-bit ARM920T core that Samsung produces The recognition devices are connected and work together to complete the recognition of the RNA secondary structure.

[0038] Both the input unit 0101 and the display unit 0106 of the host computer 01 use the input and output devices of the PC computer to realize their functions.

[0039] In the present invention, the intercommunication between the host ...

Embodiment 2

[0049] Work steps

[0050] image 3 It is a logical function diagram of the method for identifying the secondary structure of long-chain RNA with pseudoknots based on the component type of the present invention. like image 3 As shown in the logical function diagram, the steps for users to use the device to identify RNA secondary structures are as follows:

[0051] 1) Input the RNA sequence through the input unit 0101 of the host computer 01 and transmit it to the internal storage unit 0206 of the RNA secondary structure identification device through the RS-232 serial port 0105 and RS-232 serial port 0205, and further read the data into the buffer unit 0207 ;

[0052] 2) The local component processing unit 02081 reads the RNA sequence from the cache unit 0207, and uses the size set by the sliding window to intercept the component sequence, and the variation range of the component sliding window size is set to 50nt-200nt;

[0053] 3) For the above-mentioned intercepted comp...

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Abstract

The invention discloses a component-based identification method and device of long-chain RNA secondary structures with pseudo knots. A balance energy predicting method is used for predicting the RNA secondary structures, multiple-branch ring energy computing is perfected, preliminary pseudo-knot energy is added, so that energy computing is accurate and is close to reality, and the accuracy of prediction of the RNA secondary structures with the pseudo knots is improved. The problems that current secondary structure identification software is limited to overall structure accuracy attention, and the significance in biological function components and function components with conservative local structures in long-chain RNA is ignored currently are solved, and accordingly under the situation of sequence growing, the RNA secondary structures can be identified effectively. The method that software and hardware are combined is fully used, prediction time-space complexity is improved, and the device can achieve plug and play on a machine which is provided with client side software.

Description

technical field [0001] The invention discloses a recognition method and device based on a component-type long-chain RNA secondary structure with pseudoknots, and belongs to the field of bioinformatics RNA secondary structure prediction. [0002] The invention relates to a method for identifying the secondary structure of long-chain RNA with pseudoknots based on local structure components, based on equilibrium energy, and provides a device suitable for the method. Background technique [0003] Different from DNA and protein, RNA can not only carry genetic information, but also be used as a functional molecule. The function of RNA is closely related to its structure. The current research on the tertiary structure of RNA is restricted by various conditions. Therefore, the study of the secondary structure of RNA It can reveal the evolution law of RNA in the life process, which is of great significance to promote the human post-genome project and the development of medicine and b...

Claims

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Application Information

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IPC IPC(8): G06F19/18
Inventor 刘元宁张浩艾露露段云娜李志胡明刚马知行李阳
Owner JILIN UNIV
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