Genomic sequence alignment method and genomic sequence alignment device

A genome sequence and reference genome technology, applied in the field of genome sequence comparison methods and devices, can solve the problems of slow processing progress, high resource consumption, long time-consuming genome sequence comparison algorithm, etc., to shorten the comparison time and optimize the algorithm speed , the effect of improving sequencing efficiency

Active Publication Date: 2017-05-17
UNITED ELECTRONICS
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[0003] In view of this, the purpose of the present invention is to propose a genome sequence comparison method and device, which can...

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  • Genomic sequence alignment method and genomic sequence alignment device

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[0043] In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be described in further detail below in conjunction with specific embodiments and with reference to the accompanying drawings.

[0044] It should be noted that all expressions using "first" and "second" in the embodiments of the present invention are used to distinguish two entities with the same name but different parameters or parameters that are not the same, see "first" and "second" It is only for the convenience of expression, and should not be construed as a limitation on the embodiments of the present invention, which will not be described one by one in the subsequent embodiments.

[0045] Based on the foregoing objectives, the first aspect of the embodiments of the present invention proposes a genome sequence comparison method, which can solve the problems of long time-consuming, slow processing progress, and high resource consumption of gen...

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Abstract

The invention discloses a genomic sequence alignment method and a genomic sequence alignment device. The method includes: reading part of genomic sequences from to-be-aligned genomic sequence files; subjecting the part of the genomic sequences and a reference genomic sequence to alignment according to a two-way BWT alignment algorithm, a single-end dynamic programming alignment algorithm and a double-end dynamic programming alignment algorithm; after alignment is finished according to any of the alignment algorithms, if no sequence failed in alignment exists in the part of the genomic sequences, reading new part of genomic sequences from the to-be-aligned genomic sequence files, and performing alignment according to the steps; repeating the steps until alignment of all of the to-be-aligned genomic sequence files is finished, and outputting alignment results. By the genomic sequence alignment method and the genomic sequence alignment device, problems of high time consumption, low processing speed and high resource consumption of the genomic sequence alignment algorithms can be solved.

Description

technical field [0001] The invention relates to the technical field of data processing, in particular to a genome sequence comparison method and device. Background technique [0002] Genome sequence alignment is a general basic processing step in genome data analysis. The purpose of this process is to locate the position of the sequencing sequence on the reference genome. The length of the reference genome sequence of the human genome is about 3GB, and the length of the sequencing sequence is generally between 100bp and 150bp. Generally, the total amount of sequence data for whole genome sequencing is about 100GB. To compare these sequences, the industry currently generally uses open-source comparison software, such as BWA and Bowtie2, which generally take more than 10 hours to process, which is the main time-consuming step in genomic data analysis. However, these common next-generation genome sequencing sequence comparison algorithms generally have the problems of long tim...

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Application Information

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IPC IPC(8): G06F19/00
CPCG16B20/00
Inventor 何光铸王东辉蔡文君刘凯
Owner UNITED ELECTRONICS
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