Gene Sequence Input Formatting and MapReduce Computing

• Main Authors: Xiaolong Feng, Jing Gao
• Format: Article
• Language: English
• Published: Bulgarian Academy of Sciences 2019-06-01
• Series: International Journal Bioautomation
• Subjects: Input formatting; MapReduce; Gene sequence; Sequence alignment
• Online Access: http://www.biomed.bas.bg/bioautomation/2019/vol_23.2/files/23.2_10.pdf

Considering the limitations of the application programming interface (API) of Hadoop in gene sequence computing, this paper puts forward an input formatting method that reads the format of gene sequence as key-value pairs in the form of records. This method relies on the rewriting of Hadoop source code, which is an extension of platform function, and eliminates the need to preprocess data with other tools. On this basis, a MapReduce computing model was designed for distributed parallel computing of gene sequence alignment tasks. Experimental verification shows that the proposed method can read many kinds of gene sequence files effectively on Hadoop, and the proposed model can realize distributed parallel computing of gene sequence alignment. The research findings provide a valuable reference for bioinformatics computing tasks on Hadoop platform.