A method and apparatus for searching compressed nucleic acid sequences are disclosed. In the method, a reference sequence is compared with a subject sequence to be encoded, the subject sequence is compressed, an index is created with respect to the reference sequence and the compressed subject sequence, a position corresponding to a query is searched for in the compressed subject sequence using the index, a character found at the position within the compressed sequence is converted into a sequence, and the sequence is output as the response to the query.