A method and apparatus for determining similarity among gene sequences, for compressing a gene sequence, and for decompressing a gene sequence. The method for determining similarity between a first gene sequence and a second gene sequence includes: moving a sliding window of a predefined length on the first gene sequence and the second gene sequence respectively; extracting a first part String1i of the first gene sequence within the sliding window, and a second part String2i of the second gene sequence within the sliding window during the ith movement of the sliding window; and determining similarity between the first gene sequence and the second gene sequence based on the first part String1i and the second part String2i. Also provided is an apparatus for the above method.