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Method for identifying and removing tips of bidirectional multistep De Bruijn graph

A bidirectional multi-step, protruding end technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problem of reducing the reapt area and affecting the quality of the assembly, and achieve the effect of increasing the length and improving the quality.

Active Publication Date: 2014-04-02
SHENZHEN INST OF ADVANCED TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The generation of some wrong reads also resulted in a large number of branching
The smaller the K value, the more serious the branching problem, and the larger the K value, the fewer reapt areas appear, which directly affects the quality of assembly

Method used

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  • Method for identifying and removing tips of bidirectional multistep De Bruijn graph
  • Method for identifying and removing tips of bidirectional multistep De Bruijn graph

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Embodiment Construction

[0044] The present invention will be described in further detail below in conjunction with the accompanying drawings and specific embodiments.

[0045] The embodiment of the present invention provides a method for identifying and removing overhangs of a bidirectional multi-step De Bruijn graph, comprising steps,

[0046] S1. Read the sequencing data source file, and construct a bidirectional multi-step De Bruijn diagram;

[0047] S2, setting the data structure of each vertex u in the bidirectional multi-step De Bruijn graph, and identifying the bidirectional edge at the protruding end of the bidirectional multi-step De Bruijn graph;

[0048] S3. Removing the bidirectional edges at the protruding end of the bidirectional multi-step De Bruijn graph.

[0049] Among them, if a vertex u has only one bidirectional edge, and the length of the bidirectional edge is less than the length of kmer, and the weight of the bidirectional edge is less than 0.25 times the maximum weight of all...

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Abstract

The invention discloses a method for identifying and removing tips of a bidirectional multistep De Bruijn graph, which comprises the following steps of: S1, reading a sequencing data source file and constructing the bidirectional multistep De Bruijn graph; S2, setting a data structure of each vertex u in the bidirectional multistep De Bruijn graph and identifying bidirectional edges of the tips of the bidirectional multistep De Bruijn graph; and S3, removing the bidirectional edges of the tips of the bidirectional multistep De Bruijn graph. According to the invention, the tips are judged whether to be deleted on the basis of structural information of related nodes and relative abundance of the edges; a judgment of the method disclosed by the invention is finer than that of a conventional method; the method disclosed by the invention considers more information in the Bruijn graph; the bidirectional edges of the tips can be effectively deleted, so that the length of contigs can be prolonged to a certain degree and quality of contigs is synchronously improved.

Description

technical field [0001] The invention relates to the field of gene sequencing, in particular to a method for identifying and removing overhangs of a bidirectional multi-step De Bruijn graph. Background technique [0002] Gene sequence analysis takes algorithms and mathematical models as the core, including: storage and acquisition of genetic data, sequence comparison, sequencing and splicing, gene prediction, biological evolution and phylogenetic analysis, protein structure prediction, RNA structure prediction, molecular design and drugs Design, metabolic network analysis, gene chip, DNA computing, etc. The close combination of biotechnology and computer information processing technology has accelerated the speed of processing biological information data, making accurate interpretation of biology in the shortest possible time and accelerating the development of bioinformatics. [0003] Gene sequence analysis is the analysis of massive gene sequence data to extract and mine n...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/10
Inventor 孟金涛张慧琳彭丰斌魏彦杰冯圣中
Owner SHENZHEN INST OF ADVANCED TECH
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