Parallel universal sequence alignment method running on multi-core computer platform
A multi-core computer and general-purpose sequence technology, applied in computing, special data processing applications, instruments, etc., can solve the problem of low efficiency of sequence alignment
Inactive Publication Date: 2014-12-24
HUNAN UNIV
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[0011] The technical problem to be solved by the present invention is to provide a parallel universal sequence alignment method running on a multi-core computer platform to overcome the low efficiency of sequence alignment in the prior art
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Embodiment 1
[0086] The experiment tested two sets of data respectively. One set was the traditional sequence comparison Benchmarks, including BAliBASE3.0, IRMBASE2.0, PREFAB4.0 and OXBench1.3, which were used to calculate the Q / TC score of the CDAM method to evaluate its Alignment accuracy. One group uses the Rose sequence generator to generate a large-scale sequence collection, which is used to calculate the speedup ratio of the CDAM method and the MUSCLE method, so as to evaluate the efficiency of the CDAM method in processing large-scale sequence alignments.
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The invention discloses a parallel universal sequence alignment method running on a multi-core computer platform. The parallel universal sequence alignment method comprises the following steps: firstly performing classification on to-be-aligned sequence sets by utilizing a clustering method (Cluster) to obtain subsequence sets (C1, C2, ... , Cm) unequal in size; then, distributing to-be-aligned subsequence sets to all computing cores (Core1, Core2, ... , Coren) by applying a distribution method (Distribute), wherein load balance on each core is taken as the final goal of distribution; subsequently, respectively aligning (Align) all the subsequence sets by applying the traditional sequence alignment method; finally, merging aligned subsequence sets by applying a merging method (Merge) to obtain final alignment results of the to-be-aligned subsequence sets. According to the parallel universal sequence alignment method disclosed by the invention, upon the multi-core computer platform, by fully utilizing data parallel computing strategy, the processing efficiency of biological sequence alignment is obviously improved.
Description
technical field [0001] The invention belongs to the technical field of computer software, and relates to a method for comparing parallel universal sequences running on a multi-core computer platform. 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, function prediction, similarity search, biopharmaceuticals, disease diagnosis and...
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IPC IPC(8): G06F19/00
Inventor 李肯立朱香元唐卓徐雨明李克勤肖正
Owner HUNAN UNIV