Method for DNA sequencer to reattach short sequence to genome

A short-sequence, genome technology, applied in the field of DNA sequencer short-sequence paste-back genome, can solve the problem of not giving discrete seed combinations, etc.

Inactive Publication Date: 2012-05-16
DINGSHENG TECH BEIJING
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  • Abstract
  • Description
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  • Application Information

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Problems solved by technology

[0005] A method using several discrete seeds A short-sequence method that achieves 100% recall, but only provides a proof of the number of discrete seeds required, and does not give a specific combination of discrete seeds

Method used

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  • Method for DNA sequencer to reattach short sequence to genome
  • Method for DNA sequencer to reattach short sequence to genome
  • Method for DNA sequencer to reattach short sequence to genome

Examples

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Embodiment Construction

[0512] The technical solution of the present invention will be described in detail below in conjunction with the accompanying drawings.

[0513] figure 1 An embodiment of the short sequence back-posting genome method of the DNA sequencer of the present invention is shown.

[0514] First, the short sequence files generated by the DNA sequencer need to be imported. In this embodiment, the short sequences generated by the two DNA sequencers are respectively carried out, that is, the short sequence files generated by the Illumina sequencer and the AB SOLiD sequencer are imported in this step, and the short sequences are identified for short sequence posting. The data file formats generated by the Illumina GA sequencer include *_seq.txt, *_qual.txt, FASTA, and FASTQ. The data file formats generated by AB SOLiD sequencer are *.csfasta, *.qual. The file contains the name, sequence or sequencing quality score of each short sequence. Due to the difference in sequencing technology, ...

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Abstract

The invention belongs to a method for processing DNA sequencing data. In order to improve the efficiency of reattaching a short sequence to genome, the invention provides a method for a DNA sequencer to reattach a short sequence to genome. 100% recall ratio can be ensured by giving an optimized overall length discrete seed combination, and meanwhile, the efficiency of data processing is improved.

Description

technical field [0001] The invention relates to a processing method for DNA sequencing data, in particular to a processing method for the result of sequencing—short-sequence reply genome. Background technique [0002] DNA sequencing technology, that is, the technology for determining the sequence of DNA. In molecular biology research, DNA sequence analysis is the basis for further research and modification of target genes. The technologies used for sequencing mainly include the dideoxy chain terminal termination method invented by Sanger et al. (1977) and the chemical degradation method invented by Maxam and Gilbert (1977). These two methods are very different in principle, but they are all based on the fact that the nucleotide starts at a fixed point and ends at a specific base at random, resulting in four groups of A, T, C, and G with different lengths. A series of nucleotides are then detected by electrophoresis on a urea-denatured PAGE gel to obtain the DNA sequence. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G06F19/10
Inventor 马斌
Owner DINGSHENG TECH BEIJING
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