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Method for detecting DNA sequence similarity by using one-dimensional cell neural network

A technology of DNA sequence and neural network, applied in the field of DNA sequence similarity detection

Inactive Publication Date: 2014-01-29
UNIV OF ELECTRONICS SCI & TECH OF CHINA
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Problems solved by technology

[0006] When the traditional alignment algorithm solves the problem of paired sequence alignment with a large amount of data, the time and storage space required increase exponentially with the number of sequences and the length of the sequence. Therefore, we need to study better and updated A method to improve the search speed of the algorithm and reduce the calculation time

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  • Method for detecting DNA sequence similarity by using one-dimensional cell neural network
  • Method for detecting DNA sequence similarity by using one-dimensional cell neural network
  • Method for detecting DNA sequence similarity by using one-dimensional cell neural network

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[0073] The implementation process of the present invention will be further specifically described below in conjunction with two DNA base sequences that are actually taken from the NCBI database.

[0074] The selected DNA base sequence identification numbers are S62051 and NM_008134 respectively. For the convenience of display, only two sequence fragments are selected to illustrate the implementation process. The details of these two sequence fragments are shown in Table 1:

[0075] DNA base sequence

base number

Sequence base fragment code

S 1

8

AAGCTCTG

S 2

6

CAGCAT

[0076] Table 1

[0077]Two DNA sequence fragments as shown in Table 1 S 1 and S 2 , and the number of bases they contain is K 1 =8 and K 2 =6, according to the 4 sub-steps under step 3, pair S 1 and S 2 Align as follows:

[0078] ① According to step 3.1 of step (3), initialize the designed one-dimensional dual cellular neural network:

[0079] m=8+1=9...

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Abstract

The invention discloses a method for detecting DNA sequence similarity by using a one-dimensional cell neural network. The method comprises the steps of: firstly, designing a one-dimensional cell neutral network basic model and then establishing a one-dimensional dual cell neutral network by utilizing the model; then initializing the network by using information of two to-be-detected DNA sequences; recording a cell state and an output in the network at each moment during the network operation process and accordingly forming an optimized output matrix; then traversing elements in the optimized output matrix so as to determine an optimal alignment path; finally, performing blank insertion operation on the two sequences based on the alignment path so as to finish the global alignment of the two sequences conveniently; after the sequences are aligned, calculating the global similarity based on the number of aligned basic groups and the total number of the basic groups. As shown by the test and contrast, the necessary calculation time of the method for detecting the DNA sequence similarity by using the one-dimensional cell neural network is obviously reduced to a great extent than that needed by the existing method for the DNA sequences in relatively long length while the detection precision is guaranteed.

Description

technical field [0001] The invention belongs to the technical field of DNA sequence similarity detection in bioinformatics, and more specifically relates to a method for detecting DNA sequence similarity with a one-dimensional cellular neural network, which is used for detecting the global similarity of DNA double sequences . Background technique [0002] In the 1970s, the emergence of DNA sequencing methods produced a lot of biomolecular sequence data, which is growing rapidly at a geometric rate, and it has become the field with the largest amount of data generated by human practice. After the successful drawing of the human genome sequence map, people have successively launched genome sequencing projects for various animals and plants. However, data is not equal to knowledge and information. The task of researching and processing these data is getting heavier and heavier. We must find efficient ways to solve such problems. [0003] DNA generally exists in the form of do...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22G06N3/02
Inventor 纪禄平郝德水周龙黄青君尹力杨洁
Owner UNIV OF ELECTRONICS SCI & TECH OF CHINA
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