Distributed gene sequence alignment method based on Basic Local Alignment Search Tool (BLAST)

Abstract

The invention relates to the technical fields of computer and bioinformatics, disclosing a distributed gene sequence alignment method based on Basic Local Alignment Search Tool (BLAST). The method comprises the following steps: S1, the program analyzes user parameters, determines MPI thread serial number and reads query sequence file; query sequences are divided based on task number, and every MPI thread reads corresponding MPI thread serial number; S2, according to the MPI thread serial number, the program judges if the present MPI thread is head node; if the present MPI thread is a head node, the program waits for communication requests of other MPI threads; if a communication request exists, the response exists and then the present task is allocated to the thread making the request; the program continuously allocates task; if the present MPI thread is not a head node, the program requests a task serial number from the head node, reads the query sequence file segment according to the task serial number and performs BLAST to obtain BLAST alignment result; the program subtracts 1 in the task serial number and requests the task serial number after performing BLAST; and S3, the program combines all BLAST alignment results. The method can reduce hardware cost of the bioinformatics research.

Description

technical field [0001] The invention relates to the technical fields of computer and bioinformatics, in particular to a method for comparing distributed gene sequences based on BLAST. Background technique [0002] In the past few years, Next Generation Sequencing (NGS) technology has brought tremendous changes to biological research, and has made significant progress in sequencing principles, operational details, and technology expansion. Compared with the traditional Sanger sequencing method, the NGS technology platform avoids the cloning process, and directly uses adapters to perform parallel PCR (polymerase chain reaction) and sequencing reactions, so its data throughput is greatly improved, and more accurate sequencing can be performed in a shorter period of time. Much DNA is sequenced. For example, it took 13 years and hundreds of sequencers to map the first human genome using Sanger sequencing, but now NGS can complete the work in a few months. In addition, the cost ...

AI Technical Summary

Problems solved by technology

Although these parallel softwares enhance the scalability of the analysis algorithm and can be easily extended to hundreds or even thousands of processors for simultaneous execution, they have some common disadvantages: 1) Not all parallel versions can Produces the same results as the NCBI Blast stand-alone operation [4], which is caused by the use of different database cutting or result merging methods; 2) In traditional high-performance computing, shared storage systems are usually used, that is, databases, Blast binary files, sequence files, and intermediate results are all stored on the same physical storage. Although it is more convenient from the perspective of system maintenance, when the parallelism is high, the aggregated IO of all nodes has a very large overhead on network resources[ 5], will seriously affect the overall execution efficiency of the entire software, so IO bandwidth often becomes the bottleneck of multiple sequence alignment analysis; 3) These softwares all need to use highly coupled high-performance computer clusters and high-performance storage systems, and the hardware cost expensive

Images