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Method and system for optimizing multiple sequence alignment algorithms, and storage medium

A technology of sequence comparison and optimization method, applied in the field of data processing, which can solve the problems of slow processing progress, long time-consuming, and high resource consumption, and achieve the effects of shortening time-consuming, speeding up processing progress, and reducing resource consumption

Active Publication Date: 2019-06-28
INST OF SPECIAL ANIMAL & PLANT SCI OF CAAS
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Problems solved by technology

However, due to the large amount of sequence data of the reference genome sequence and sequencing sequence, the processing time for comparing sequences is relatively long, and the establishment of the most time-consuming process in genome data analysis is obviously time-consuming, slow in processing progress, and consumes a lot of resources. The method can no longer meet the needs of sequence comparison

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  • Method and system for optimizing multiple sequence alignment algorithms, and storage medium
  • Method and system for optimizing multiple sequence alignment algorithms, and storage medium
  • Method and system for optimizing multiple sequence alignment algorithms, and storage medium

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Embodiment Construction

[0051] The following will clearly and completely describe the technical solutions in the embodiments of the present invention with reference to the drawings in the embodiments of the present invention. Obviously, the described embodiments are part of the embodiments of the present invention, not all of them. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without making creative efforts shall fall within the protection scope of the present invention.

[0052] like figure 1 The optimization method 100 for a multiple sequence alignment algorithm includes:

[0053] 110. Select a core sequence from multiple sequences.

[0054] 120. Align the core sequence with other sequences in multiple sequences to obtain the number of fragments shared by the sequences.

[0055] 130. Build a first guide tree according to the number of fragments shared by any pair of sequences.

[0056] 140. Obtain the first result of mult...

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Abstract

The invention relates to a method and a system for optimizing multiple sequence alignment algorithms, and a storage medium. The method comprises the steps of selecting a core sequence from multiple sequences; performing pairwise alignment on the core sequence and other sequences in the multiple sequences, and obtaining the number of common fragments of the sequences; constructing a first guiding tree according to the number of common fragments of the pairwise sequences; performing a progressive algorithm on the first guiding tree for obtaining a first result through alignment of multiple sequences; calculating the distance between the pairwise sequences according to the first result, and obtaining a distance matrix; constructing a second guiding tree according to the distance matrix, comparing the first guiding tree with the second guiding tree, performing re-alignment on the sequences which correspond with the changing part for obtaining a second result, and repeating processes of constructing the second guiding tree and comparing the first guiding tree with the second guiding tree until the number of comparison times exceeds a threshold, thereby shortening time consumption in sequence comparison, increasing processing process and reducing resource consumption.

Description

technical field [0001] The invention relates to the technical field of data processing, in particular to an optimization method and system for a multiple sequence alignment algorithm, and a storage medium. Background technique [0002] The general basic processing steps of genome data analysis for genome sequence alignment. The purpose of this process is to locate the sequencing sequence and then refer to the position on the genome. However, due to the large amount of sequence data of the reference genome sequence and sequencing sequence, the processing time for comparing sequences is relatively long, and the establishment of the most time-consuming process in genome data analysis is obviously time-consuming, slow in processing progress, and consumes a lot of resources. The method can no longer meet the needs of sequence comparison. Contents of the invention [0003] The technical problem to be solved by the present invention is to provide an optimization method, system a...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B40/00
Inventor 廉士珍闫喜军朱言柱白雪薛向红闫鸣昊吕爽
Owner INST OF SPECIAL ANIMAL & PLANT SCI OF CAAS
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