Method for accelerating RNA secondary structure prediction based on stochastic context-free grammar

A secondary structure and context technology, applied in the direction of machine execution devices, biochemical equipment and methods, microbial measurement/inspection, etc., can solve the problem that does not involve three-dimensional dynamic programming matrix hardware acceleration, and has no RNA secondary structure prediction acceleration Methods and other issues

Inactive Publication Date: 2010-06-02
NAT UNIV OF DEFENSE TECH
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Problems solved by technology

However, the existing hardware acceleration methods in the field of sequence comparison, search and RNA structure prediction are limited to the parallelization of two-dimensional dynamic programming matrix, and do not

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  • Method for accelerating RNA secondary structure prediction based on stochastic context-free grammar
  • Method for accelerating RNA secondary structure prediction based on stochastic context-free grammar
  • Method for accelerating RNA secondary structure prediction based on stochastic context-free grammar

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Embodiment Construction

[0072] figure 1 It is the overall structure diagram of the heterogeneous computer system constructed in the first step of the present invention. The heterogeneous computer system consists of a host computer and a reconfigurable algorithm accelerator. The reconfigurable algorithm accelerator is inserted into the PCI-E slot of the host motherboard and connected to the host. A CM model formatting program, an RNA sequence coding program, a reconfigurable algorithm accelerator logic download program and a data communication program are installed on the host computer. The host configures the algorithm FPGA in the reconfigurable algorithm accelerator through the JTAG programming cable, loads the RNA sequence and CM model to the reconfigurable algorithm accelerator through the PCI-E interface, and starts the reconfigurable algorithm accelerator; the reconfigurable algorithm accelerator Complete the calculation of the CYK / inside algorithm without backtracking, and then return the co...

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Abstract

The invention discloses a method for accelerating RNA secondary structure prediction based on stochastic context-free grammar (SCFG), aiming at accelerating the speed of RNA secondary structure predication by using the SCFG. The method comprises the following steps of: firstly establishing a heterogeneous computer system comprising a host computer and a reconfigurable algorithm accelerator, then transmitting a formatted CM model and an encoded RNA sequence into the reconfigurable algorithm accelerator through the host computer, and executing a non-backtrace CYK/inside algorithm calculation by a PE array of the reconfigurable algorithm accelerator, wherein task division strategies of region-dependent segmentation and layered column-dependent parallel processing are adopted in the calculation so as to realize fine-grained parallel calculation, and n numbers of PEs simultaneously calculate n numbers of data positioned different columns of a matrix by adopting an SPMD way, but different calculation sequences are adopted in the calculation according to different state types. The invention realizes the application acceleration of the RNA sequence secondary structure prediction based on the SCFG model and has high acceleration ratio and low cost.

Description

technical field [0001] The invention relates to a method for accelerating RNA secondary structure prediction based on a random context-free grammar SCFG (Stochastic Context-free Grammars) model. Background technique [0002] With the completion of genome sequencing projects for humans and other species, bioinformatics research has entered the post-genome era. Sequence alignment and search have become the most important basic work in the field of molecular biology. At present, there are many classic research tools in the field of DNA and protein sequence analysis, such as BLAST, FASTA, HMMER, ClustalW, etc. Since the discovery of RNA with catalytic properties in the mid-1980s, various important biochemical functions of RNA have gradually attracted people's attention. Different from the double helix structure of DNA sequence, although RNA sequence itself is a single strand, it can form a two-dimensional or even three-dimensional structure through complementary base pairing. ...

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Application Information

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IPC IPC(8): C12Q1/68G06F19/00G06F9/38
Inventor 夏飞窦勇姜晶菲周杰邬贵明雷元武
Owner NAT UNIV OF DEFENSE TECH
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