Accelerating device for gene comparison algorithm

A technology of gene comparison and acceleration device, applied in the fields of bioinformatics, informatics, instruments, etc., can solve the problems of power consumption, low computing density, electrical characteristics limitation, etc. The effect of limited memory access bandwidth

Active Publication Date: 2019-05-21
INST OF COMPUTING TECH CHINESE ACAD OF SCI
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Problems solved by technology

[0003] In the prior art, the gene comparison algorithm usually adopts a general-purpose processing structure (such as a common server, etc.), and there are two main problems in this gene comparison algorithm: 1), the CPU and the memory are usually separated. The memory interface to access data is limited by electrical characteristics, and the memory access bandwidth is limited; in addition, due to the poor locality of the gene comparison operation program, there is a great demand for memory bandwidth. This demand for high bandwidth is different f

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  • Accelerating device for gene comparison algorithm
  • Accelerating device for gene comparison algorithm
  • Accelerating device for gene comparison algorithm

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Embodiment Construction

[0034] In order to make the objectives, technical solutions, design methods and advantages of the present invention clearer, the present invention will be further described in detail below through specific embodiments in conjunction with the accompanying drawings. It should be understood that the specific embodiments described herein are only used to explain the present invention, but not to limit the present invention.

[0035] figure 1 A structural diagram of an acceleration device oriented to a gene alignment algorithm according to an embodiment of the present invention is shown. The acceleration device 100 includes a host terminal 110 (host) and a plurality of acceleration modules (Cubes) 120 (4 cubes are shown, i.e. Cube 0 to Cube 3).

[0036] There is a communication connection between the host terminal 110 and the acceleration module 120. The host terminal 110 is used for distributing and controlling the gene sequencing sequence of the acceleration module 120, and can ...

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Abstract

The invention provides an accelerating device for a gene comparison algorithm. The accelerating device comprises a host terminal and a plurality of accelerating modules. Each accelerating module comprises a plurality of storage layers, a vertical slice management unit and a switching network. The host terminal is used for controlling distribution of gene sequencing sequences to the accelerating modules and receiving of gene comparison results. The storage layers of the accelerating modules are used for storing gene reference sequences. The vertical slice management units of the accelerating modules are used for managing slices formed by vertically dividing the plurality of storage layers and executing a gene comparison algorithm to obtain a gene comparison result. The switching networks ofthe accelerating modules are used for controlling data exchange inside the accelerating modules and data exchange between the accelerating modules and the outside. The accelerating device disclosed by the invention can improve the processing speed of a gene comparison algorithm by utilizing a customized structure.

Description

technical field [0001] The invention relates to the technical field of biological gene data processing, in particular to an acceleration device oriented to a gene comparison algorithm. Background technique [0002] At present, the development of biotechnology is triggering an industrial revolution in the fields of agriculture, medicine, energy, and materials, effectively alleviating the problems of food, health, and resources, and has a broad space for development. The importance of bioinformatics as a discipline in the biological field is also increasingly prominent. It is one of the major frontier fields of life sciences and natural sciences. Its research focuses on genomics and proteomics, specifically from nucleic acid and protein sequences. As a starting point, the biological information of the structure-function expressed in the sequence is analyzed. In sequence (read) analysis, gene alignment is the most basic and most commonly used method. Through gene alignment, th...

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Application Information

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IPC IPC(8): G16B30/00
Inventor 臧大伟王元戎沈华谭光明刘伯然孙凝晖
Owner INST OF COMPUTING TECH CHINESE ACAD OF SCI
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