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

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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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 involve the hardware acceleration of three-dimensional dynamic programming matrix, and there is no use of FPGA devices to realize the Related reports on SCFG's accelerated method for RNA secondary structure prediction

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