A method of searching a pattern in sequence data includes setting a plurality of interest pattern models each including an interest pattern length, an allowed mismatch value, and a minimum support; calculating a support of a candidate pattern that is generable within the interest pattern length based on the allowed mismatch value of at least one of the plurality of interest pattern models; and determining whether the support of the candidate pattern fulfills a condition of the minimum support of at least one of the plurality of interest pattern models.