DNA methylation data detection method and device thereof based on seed sequence information

A sequence information and data detection technology, applied in the field of bioinformatics, can solve the problems of low precision, large amount of data, missing sites in the methylation detection region, etc., and achieve improved utilization, convenient research, and shortened comparison operations Effect

Active Publication Date: 2018-06-19
THE THIRD AFFILIATED HOSPITAL OF GUANGZHOU MEDICAL UNIVERSITY
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Problems solved by technology

[0004] However, the existing tools and algorithms for locating DNA methylation sites have the following defects in the actual use process: when comparing DNA base sequences, the accuracy is not high, and the operation time is long due to the la

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  • DNA methylation data detection method and device thereof based on seed sequence information
  • DNA methylation data detection method and device thereof based on seed sequence information
  • DNA methylation data detection method and device thereof based on seed sequence information

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Embodiment 1

[0071] refer to figure 2 , the first embodiment of the present invention provides a method for detecting DNA methylation data of seed sequence information, comprising:

[0072] Step S100, constructing an index database;

[0073] As mentioned above, in this embodiment, the index database is the reference genome sequence information of the species containing the target sample to be tested. For example, the target sample to be tested is the DNA of the Kunming S180 rat, and then the reference genome sequence information of the relevant rodent is imported. As a comparison reference.

[0074] Step S200, obtaining the sequencing data of the target sample, and segmenting the sequencing data according to the preset seed sequence length to obtain segmented seed sequence information;

[0075] As mentioned above, it needs to be understood that, so far, the bisulfite sequencing method is a relatively efficient method for detecting DNA 5mC base modification, which can directly detect the...

Embodiment 2

[0084] refer to image 3 , the second embodiment of the present invention provides a DNA methylation data detection method for seed sequence information, based on the above figure 2 In the first embodiment shown, the step S100 includes:

[0085] Step S110, obtaining the reference gene sequence of the species to which the target sample belongs;

[0086] As mentioned above, before performing the methylation mapping of the target sample, it is necessary to construct an index database, and write the reference genome sequence file of the research species corresponding to the target sample into the memory.

[0087] Step S120, segmenting the reference gene sequence according to the length of the preset seed sequence to obtain a reference seed sequence;

[0088] As mentioned above, the reference gene sequence is a long string of four letters representing four bases ATCG. Taking the human reference genome as an example, the actual length is about 3×10 9 bp. The idea of ​​encoding ...

Embodiment 3

[0096] refer to Figure 4 , the third embodiment of the present invention provides a DNA methylation data detection method for seed sequence information, based on the above figure 2 In the first embodiment shown, the step S200 includes:

[0097] Step S210, performing sequencing on the target sample to obtain sequencing data of the target sample;

[0098] As mentioned above, the target sample is sequenced, that is, as Figure 10 As shown, the target sample to be sequenced is treated with bisulfite, and high-throughput sequencing is performed by a next-generation sequencer to obtain the target sample sequencing data. Among them, the sequence information showing DNA will change, the original non-methylated cytosine becomes uracil, and the sequencing result is reflected into thymine, while the methylated cytosine and other bases remain unchanged.

[0099] Step S220, according to the preset seed sequence length, segment the target sample sequencing data segment by segment from ...

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Abstract

The invention provides a DNA methylation data detection method and a device thereof based on seed sequence information. The method comprises the steps of building an index database; obtaining sequencing data of a target sample, and according to the preset seed sequence length, dividing the sequencing data to obtain divided seed sequence information; based on the index database, determining comparison candidate position information of each divided seed sequence information; conducting system evaluation on each comparison candidate position information to obtain a system evaluation result, and according to the system evaluation result, obtaining a DNA methylation locus of the target sample. Time of comparison operation which consumes most time in data analysis is greatly shortened, on the basis of guaranteeing the integrity of a methylation detection area locus, the utilization rate of data is increased by a large margin, the operation efficiency and accuracy of the data are improved bya large margin, and great convenience is brought to further research on DNA nucleobase modification information for scientific research staff in the field of life science.

Description

technical field [0001] The present invention relates to the technical field of biological information, more specifically, to a method and device for detecting DNA methylation data based on seed sequence information. Background technique [0002] DNA base modification has been one of the research hotspots in the field of life sciences in recent years, among which the dynamic modification of methylation on the fifth carbon atom of cytosine (5mC) has been studied in depth. 5mC is the process of selectively adding a methyl group to cytosine to form 5-methylcytosine under the action of DNA methyltransferase. When it was discovered, it was defined as the fifth base. In fact, it is a An important epigenetic mark that plays an important role in biological processes such as regulation of gene expression, maintenance of chromatin structure, gene imprinting, X chromosome inactivation, and embryonic development. DNA methylation, as a heritable epigenetic modification, is stably transmi...

Claims

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Application Information

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IPC IPC(8): G06F19/28G06F19/20
CPCG16B25/00G16B50/00
Inventor 晏光荣朱卉芳韩悦
Owner THE THIRD AFFILIATED HOSPITAL OF GUANGZHOU MEDICAL UNIVERSITY
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