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Sequence alignment Seed processing method, system and device and readable storage medium

A technology for sequence alignment and processing methods, applied in sequence analysis, bioinformatics, informatics, etc.

Active Publication Date: 2020-03-31
LANGCHAO ELECTRONIC INFORMATION IND CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, such a Seed will have a large number of hits on the reference sequ

Method used

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  • Sequence alignment Seed processing method, system and device and readable storage medium
  • Sequence alignment Seed processing method, system and device and readable storage medium
  • Sequence alignment Seed processing method, system and device and readable storage medium

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Embodiment Construction

[0065] The following will clearly and completely describe the technical solutions in the embodiments of the present invention with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only some, not all, embodiments of the present invention. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without making creative efforts belong to the protection scope of the present invention.

[0066] The embodiment of the present invention discloses a Seed processing method for sequence alignment, see figure 1 As shown, the method includes:

[0067] S11: Find the candidate alignment position of each Seed in the Seed set of the sequences to be aligned in the CAL table.

[0068] Specifically, the length of a Seed is preset, and the preset length of the Seed is shifted bit by bit from the starting position of the sequence to be compared to obtain mult...

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Abstract

The invention discloses a sequence alignment Seed processing method, system and device and a computer readable storage medium. The method comprises the steps: according to the to-be-compared sequenceposition of the Seeds on a to-be-compared sequence and the candidate comparison position of the Seeds on the reference sequence, determining the linear Seeds with the consistent relative relationshipbetween the two positions of the Seeds; splicing the linear Seeds to obtain a new spliced Seed; screening out the longest Seed covering the longest base of the same base fragment of the to-be-comparedsequence from a Seed set comprising the spliced Seeds and nonlinear Seeds; further screening out the Seed which covers the target basic group fragment in each target basic group fragment on the to-be-compared sequence and of which the termination position is greater than the invalid Seed from the Seed set; synthesizing the target Seed of each target base fragment to obtain a target Seed set, wherein the target Seed set does not include Seeds in the longest Seed set, and the number of Seeds used when a subsequent sequence alignment algorithm is expanded is comprehensively reduced, so the calculated amount of an alignment system is reduced, and the matching precision and the processing performance of gene sequence alignment are improved.

Description

technical field [0001] The present invention relates to the interdisciplinary field associated with computer technology and biological gene technology, in particular to a seed processing method, system, device and computer-readable storage medium for sequence alignment. Background technique [0002] With the rapid development of biological gene detection technology, it is becoming more and more mature to extract individual genes for comparison of gene sequences, predict the possibility of suffering from various diseases, lock the genes of individual diseases, and prevent and treat them in advance. The human gene pool is currently about 3 billion base pairs, and it takes a few days to complete the comparison of a person's gene sequence using a general-purpose computer software processing platform. The traditional CPU processing platform can no longer meet the demand for fast and real-time acquisition of gene comparison results. The computing performance requirements of the p...

Claims

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Application Information

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IPC IPC(8): G16B30/10
CPCG16B30/10
Inventor 赵健史宏志崔星辰
Owner LANGCHAO ELECTRONIC INFORMATION IND CO LTD
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