Opti-SW: An improved gene sequence alignment algorithm

Opti-SW: An improved gene sequence alignment algorithm

Leixiao Li Jing Gao Yanfeng Liu 

College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China

College of Data Science and Application, Inner Mongolia University of Technology, Hohhot 010080, China

Inner Mongolia Autonomous Region Engineering & Technology Research Center of Big Data Based Software Service, Hohhot 010080, China

Corresponding Author Email: 
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This paper aims to improve the speed and complexity of Smith-Waterman (SW) algorithm. For this purpose, the SW algorithm was improved by reducing the complexity and task load of the computation of the scoring matrix without sacrificing the alignment accuracy. Then, the optimized algorithm, denoted as the Opti-SW, was verified through experiment. The results show that the Opti-SW boasts low time complexity, fast computing speed and light computing load. The research findings shed new light on the database search for gene sequences.


gene sequence alignment, smith-waterman (SW) algorithm, optimization, opti-SW

1. Introduction
2. SW algorithm
3. Improvement of the SW algorithm
4. Experiment and results analysis
5. Conclusions

The work is funded in part by the National Natural Science Foundation of China (NSFC) under Grant No. 61462070, the Doctoral research fund project of Inner Mongolia Agricultural University under Grant No. BJ09-44 and the Inner Mongolia Autonomous Region Key Laboratory of big data research and application for agriculture and animal husbandry.


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