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Large-scale distributed parallel acceleration method and system for protein identification

A protein identification, large-scale technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve problems such as poor acceleration efficiency

Active Publication Date: 2014-03-26
INST OF COMPUTING TECH CHINESE ACAD OF SCI
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Problems solved by technology

[0008] The purpose of the present invention is to provide a large-scale distributed parallel acceleration method and system for protein identification, which is used to solve the problem of poor acceleration efficiency in the prior art under the parallel condition of reaching a hundred-core or even exceeding a thousand-core processor scale

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Embodiment Construction

[0077] The present invention will be described in detail below in conjunction with the accompanying drawings and specific embodiments, but not as a limitation of the present invention.

[0078] Such as figure 1 As shown, it is a flow chart of the large-scale distributed parallel acceleration method for protein identification of the present invention. The process uses the following operations to perform large-scale distributed parallel acceleration of protein identification. The specific steps are as follows:

[0079] Step 101, first set the necessary search parameters;

[0080] Step 102, then input the protein sequence, use multiple processor processes in the cluster to theoretically digest the protein sequence, sort the obtained peptide sequences according to the theoretical precursor ion mass, remove redundancy, and finally create a peptide index file block, and Generate peptide index metadata files from peptide index file blocks;

[0081] Step 103, next analyze the input ...

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Abstract

The invention relates to a large-scale distributed parallel acceleration method and a large-scale distributed parallel acceleration system for protein identification. The method comprises the following steps of: 1, performing theoretical enzyme digestion on a protein sequence to obtain a peptide sequence, and sequencing the peptide sequence and removing redundancy of the peptide sequence to establish a peptide index file block; 2, sequencing a mass spectrogram by using a parallel processing method, and equally dividing the sequenced mass spectrogram to obtain a plurality of spectrogram data blocks; 3, uniformly distributing the spectrogram data blocks to a plurality of master processes, sequencing the distributed spectrogram data blocks by each master process, and designating the distributed spectrogram data blocks to idle slave processes in turn to perform peptide spectrogram matching identification; and 4, gathering identification results by using the parallel processing method, deducing a corresponding protein sequence by using the peptide sequence obtained through identification, and generating an output file. By the method and the system, when the scale of processor cores reaches several hundreds or even more than one thousand, satisfied acceleration efficiency can be achieved by performing the protein identification.

Description

technical field [0001] The invention relates to a distributed parallel acceleration method for large-scale protein identification, in particular to a method and a system for effectively sharing search tasks on multiple computing nodes by using distributed parallel technology to increase the speed of protein identification. Background technique [0002] A "Proteome" describes the ensemble of proteins expressed at a given moment and under given conditions in a particular biological sample. As the name suggests, proteomics is the study of the proteome. Its most basic task is to determine which proteins are expressed in the organism, how much they are expressed, post-translational modifications, and protein-protein interactions, etc., thereby obtaining protein levels. A holistic and comprehensive understanding of disease occurrence, cell metabolism and other processes in the world. In current proteome research, protein identification based on tandem mass spectrometry is one of ...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/18
Inventor 王乐珩王文平迟浩吴妍洁周郴付岩孙瑞祥贺思敏
Owner INST OF COMPUTING TECH CHINESE ACAD OF SCI
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