Three-level flow sequence comparison method based on many-core co-processor

Abstract

The invention discloses a three-level flow sequence comparison method based on a many-core co-processor. The purpose of increasing the comparison speed of sequence comparison software is achieved. According to the technical scheme, sequence comparison is performed in a multi-threading manner by an MIC (microwave integrated circuit) many-core co-processor; three serial steps of reading sequences from a main memory to an MIC, comparing the sequences and writing a comparison result to the main memory in a sequence comparison process of the MIC are in a three-level flow mode, namely, sequences required for next comparison are read during sequence comparison, a previous comparison result is written into the main memory, and a reading and writing operation and a comparison operation are carried out simultaneously. By the three-level flow sequence comparison method based on the many-core co-processor, three main processes of sequence reading, sequence comparison and comparison result returning are carried out simultaneously, the comparison efficiency is improved, and the comparison time is shortened. Compared with a two-channel eight-core CPU (central processing unit), the three-level flow sequence comparison method has the advantages that the speed of a comparison process can be increased 2.3 times at least, a large amount of memory space is prevented from being copied, and the space-time efficiency of a procedure is improved.

Description

technical field

[0001] The invention relates to a sequence alignment method in the field of biological information, in particular to a sequence alignment method based on a many-core coprocessor. Background technique

[0002] Molecular biology is a subject that studies the material basis of life phenomena at the molecular level. By studying the principles of the structure, function and synthesis of biomolecules, the functions and traits of organisms can be analyzed and analyzed in unprecedented molecular detail. understanding, and then more scientifically and rigorously clarify the nature of life phenomena.

[0003] In molecular biology research, DNA sequence analysis is the basis for further research and modification of target genes. DNA (deoxyribonucleic acid) is a biological macromolecule, which is divided into four bases, which are recorded as A, T, C, and G. The arrangement order of these macromolecules determines a certain genetic instruction, and these genetic instruc...

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