Sequence alignment method based on cpu+gpu heterogeneous system
A sequence alignment and heterogeneous system technology, applied in interdisciplinary fields, can solve the problem of low execution efficiency of large-scale sequence alignment
Active Publication Date: 2018-09-28
ZHAOQING UNIV
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[0010] The technical problem to be solved by the present invention is to provide a large-scale sequence alignment method running on a CPU+GPU heterogeneous system to overcome the low efficiency of large-scale sequence alignment in the prior art
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Embodiment 1
[0093] The experiment tested two sets of data respectively. One set is the traditional sequence alignment Benchmarks, including BAliBASE3.0, IRMBASE2.0, PREFAB4.0 and OXBench1.3, which are used to calculate the Q / TC score of the CUDA-MAFFT method, with Evaluate its alignment accuracy. A set of large-scale sequence collections obtained by randomly searching the NCBI non-redundant protein sequence database is used to calculate the acceleration ratio of the CUDA-MAFFT method and the MAFFT method to evaluate the efficiency of the CUDA-MAFFT method for large-scale sequence alignment.
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The invention discloses large-scale bio-sequence alignment and a parallel processing method for large-scale bio-sequence alignment based on a heterogeneous system. The method comprises the following steps of firstly, carrying out optimized storage on a sequence and designing a load balancing method of the heterogeneous system; secondly, designing a memory optimization method of the heterogeneous system, which consists of a sequence storage method capable of meeting combined access conditions, a similar matrix storage and access method and score matrix compression storage, for solving low actual calculated performance caused by deficiency of a storage space of the heterogeneous system; and lastly, putting forward a coarseness sequence alignment parallel method based on internal memory pre-allocation and reuse strategies. The method is based on a CPU (Central Processing Unit) and GPU (Graphics Processing Unit) heterogeneous computing platform, and load balancing and internal memory optimization technologies are fully utilized, so that the processing efficiency for large-scale bio-sequence alignment is remarkably improved.
Description
technical field [0001] The invention belongs to the interdisciplinary field related to computer technology and biological gene technology, and relates to a sequence comparison method running on a CPU+GPU heterogeneous system, especially a large-scale sequence comparison method. Background technique [0002] Sequence is the carrier of biological information, including DNA (deoxyribonucleic acid), RNA (ribonucleic acid) and protein. Biological sequence alignment (sequence alignment) takes the sequence as the research object. By comparing the correspondence between the characters in the sequence or the comparative arrangement of the characters, the similarity between the sequences is found, the difference between the sequences is identified, and its structure is speculated. , function, and evolutionary linkages. Sequence alignment is one of the most important research directions in the field of biological sequence analysis, and has been widely used in evolutionary analysis, fu...
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IPC IPC(8): G06F19/22
Inventor 朱香元
Owner ZHAOQING UNIV