Abstract: With the continuous development of bioinformatics, traditionally biological sequence analysis methods are insufficient to deal with the increasingly complex and huge biological data. In the face of this situation, deep learning has been gradually applied in biological analysis and made a series of progresses, which has become a hot research topic in biological data analysis with its advantages in processing high-dimensional data. The current research status was reviewed to better understand the new development of deep learning in the field of bioinformatics data analysis. First, the importance of applying deep learning were introduced. Second, representative deep learning models in the current application fields was described. Then, the application research status of deep learning in this field was analyzed. Finally, current limitations of deep learning in the bioinformatics field and the factors that should be considered in future development were illustrated in this paper.