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Parallel sequence alignment method and device based on load balancing and computer equipment

A sequence comparison and load balancing technology, applied in the computer field, can solve problems such as low utilization of computing resources and long time-consuming algorithm operation, and achieve the effect of improving operating efficiency

Active Publication Date: 2021-05-07
NAT UNIV OF DEFENSE TECH
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

The existing technology has the problems of long time-consuming algorithm operation and low utilization of computing resources

Method used

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  • Parallel sequence alignment method and device based on load balancing and computer equipment
  • Parallel sequence alignment method and device based on load balancing and computer equipment
  • Parallel sequence alignment method and device based on load balancing and computer equipment

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Embodiment Construction

[0062] In order to make the purpose, technical solution and advantages of the present application clearer, the present application will be further described in detail below in conjunction with the accompanying drawings and embodiments. It should be understood that the specific embodiments described here are only used to explain the present application, and are not intended to limit the present application.

[0063] The load balancing-based parallel sequence alignment method provided in this application can be applied to the following application environments. By starting the process on each node of the cluster, the files to be compared are evenly divided according to the file data volume, and the sequence comparison of the same data volume is performed on each process, and the read segment corresponding to the process is obtained according to the number of the process in the cluster The starting position of the pointer and the end position of the pointer of the file, and multi...

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Abstract

The invention relates to a parallel sequence comparison method and device based on load balancing, computer equipment and a storage medium. The method comprises the following steps: starting a process on each node of a cluster, equally dividing a to-be-compared file according to the data volume of the file, executing sequence comparison of equal data volume on each process, obtaining a pointer starting position and a pointer ending position of a read file corresponding to the process according to the serial number of the process in the cluster, and starting a plurality of threads in the process at the same time, performing parallel comparison on the sequences in the read file, and finally merging sequence comparison results output by each process to obtain a parallel sequence comparison result of load balance realized on the cluster. By means of the method, computing resources can be fully utilized, on one hand, load balancing is achieved among multiple nodes, on the other hand, parallel sequence alignment is achieved through multiple processes and multiple threads, and the operation efficiency of the algorithm is improved.

Description

technical field [0001] The present application relates to the field of computer technology, in particular to a load balancing-based parallel sequence comparison method, device, computer equipment and storage medium. Background technique [0002] Sequence alignment is one of the most basic and important operations in bioinformatics. Its fundamental task is to find the similarities and differences among organisms by comparing the sequences of biomolecules. Through sequence comparison, the structural and functional similarities in biological sequences can be found, as well as the genetic and evolutionary information of organisms. [0003] The sequence alignment algorithm based on the hash index reduces the comparison time by filtering out obviously incorrect positions, and accelerates the process of subsequence alignment by constructing a hash index on the reference genome. [0004] Algorithms such as rHAT and minimap2 have used multi-threaded methods for parallel acceleration...

Claims

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Application Information

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IPC IPC(8): G06F9/50G16B30/10
CPCG06F9/505G06F9/5061G16B30/10
Inventor 夏泽宇张昂杨灿群崔英博黄春唐滔彭林方建滨张鹏龙思凡
Owner NAT UNIV OF DEFENSE TECH
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