Spark-based Parallelization of Basic Local Alignment Search Tool

Spark-based Parallelization of Basic Local Alignment Search Tool

Blog Article

Sequence alignment is a key link of bioinformatics analysis.The basic local alignment search tool (BLAST) is a popular sequence alignment algorithm with high accuracy.However, the BLAST is inefficient in comparing and analyzing a massive amount of gene sequencing data.To solve the problem, this paper designs a Children Probiotics distributed parallel BLAST method called SparkBLAST, based on the big data technique Spark.Under the in-memory computing framework Spark, SparkBLAST identifies the task of sequence alignment, divides the sequence dataset, and compares the sequence data.

The Apache Hadoop YARN was adopted to task scheduling and resource allocation.Finally, the SparkBLAST was compared ORGANIC CONCORD GRAPE with standalone BLAST through experiments.The results show that SparkBLAST realized the speedup ratio of 3.95, without sacrificing the accuracy.In other words, SparkBLAST greatly outshines the standalone BLAST in calculation efficiency.

The research findings provide bioinformatics researchers a highly efficient tool for sequence alignment.