21. The method of claim 1 , wherein before the step of comparing, further comprising the step of aligning the input sequence SSM Matrix and the known sequence SSM Matrix.
21. The method of claim 1 , wherein before the step of comparing, further comprising the step of aligning the input sequence SSM Matrix and the known sequence SSM Matrix. 22. The method of claim 21 , wherein the step of aligning comprises the steps of: determining a union of input sequence elements and known sequence elements; inserting empty rows and columns in the input sequence SSM Matrix if the input sequence SSM Matrix does not contain all of the union; inserting empty rows and columns in the known sequence SSM Matrix if the known sequence SSM Matrix does not contain all of the union; and wherein the steps of inserting are done such that the input sequence SSM Matrix and the known sequence SSM Matrix are sorted for rows and columns in a same order.