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System for identifying coding region and non-coding region in DNA (Deoxyribose Nucleic Acid) gene sequence

A technology of DNA sequence and coding region, which is applied in the system field of identifying coding region and non-coding region in DNA gene sequence, which can solve the problems of floating-point calculation cost and excessive calculation time, and achieve the effect of small amount of calculation and high precision

Inactive Publication Date: 2015-03-11
NANJING INST OF TECH
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Problems solved by technology

All DFT operations are floating-point operations, and floating-point operations consume a lot of computing time

Method used

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  • System for identifying coding region and non-coding region in DNA (Deoxyribose Nucleic Acid) gene sequence
  • System for identifying coding region and non-coding region in DNA (Deoxyribose Nucleic Acid) gene sequence
  • System for identifying coding region and non-coding region in DNA (Deoxyribose Nucleic Acid) gene sequence

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Embodiment Construction

[0037] Preferred embodiments of the present invention will be described in detail below in conjunction with the accompanying drawings.

[0038] Based on Ramanujan sum and Ramanujan coefficients, the embodiment proposes the concept of discrete Ramanujan transform spectrum. By using the Voss numerical representation, the character DNA sequence is mapped to the numerical DNA sequence, thereby obtaining the discrete Ramanujan spectrum of the numerical DNA sequence.

[0039] Since the spectrum of the discrete Fourier transform of protein-coding sequences has a significant 3-periodicity, this is the basis for the discrete Fourier transform to be used in DNA sequence analysis. It uses the signal-to-noise ratio of the sequence at N / 3 frequency as a measure, where N refers to the length of the sequence. The examples indicate that 3-periodicity can be identified by a prominent peak at 3 in the discrete Ramanujan spectrum of protein coding sequences. As a numerical measure, the signal-...

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Abstract

The invention provides a system for identifying a coding region and a non-coding region in a DNA (Deoxyribose Nucleic Acid) gene sequence. The DRT (Discrete Fourier Transform) spectrum of a DNA sequence is calculated, and a judgment on whether the sequence is an exon or an intron is made through comparison of spectral values on k=3 and other places; if the value of the DRT spectrum on k=3 is higher than the values of other places, the sequence is the exon; otherwise, the sequence is the intron. The coding region and the non-coding region of proteins are distinguished through the discrete Ramanujan spectrum of a numerical sequence and the signal to noise ratio. A test result shows the reliability of a method disclosed by the invention. In comparison to Fourier transform, the calculation amount of the discrete Ramanujan spectrum is smaller, and the accuracy is higher.

Description

technical field [0001] The present invention relates to a system for identifying coding regions and non-coding regions in DNA gene sequences. Background technique [0002] With the advancement of science and technology, modern biological technology has been flourishing. More and more mathematical methods and signal processing techniques are applied to the research field of life sciences, forming the frontier discipline of bioinformatics. [0003] Discrete Fourier transform (DFT) is mostly used now as a method for identifying coding regions and non-coding regions in DNA gene sequences. Because this method uses floating-point operations, and the calculation accuracy of computers is limited, there are calculation errors. And floating-point operations consume a lot of computing time. [0004] First, modern computers store real numbers with a finite number of bits, which leads to rounding errors. For the discrete Fourier transform (DFT), the basis functions It is approximate...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
Inventor 滑伟
Owner NANJING INST OF TECH
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