With the rapid development of high-throughput OMICs technology in past few years, the research methodologies of life science have undergone tremendous changes. The analysis of numerous biological data urgent modern technologies and tools for big data analysis. Compared with other computing technologies, GPU has significant advantages on floating operations, parallelism and energy consumption and gets more and more attention as a generalpurpose computing device. Bioinformatics researchers apply GPU in their project and accelerate the program with a speedup of two orders of magnitude as usual. In this paper, we will review GPU application in several fields of bioinformatics and discuss the features of problems which GPU is capable of and its shortcomings.