Human Gene Functions(JAVA版)

Given two genes AGTGATG and GTTAG, how similar are they? One of the methods to measure the similarity of two genes is called alignment. In an alignment, spaces are inserted, if necessary, in appropriate positions of the genes to make them equally long and score the resulting genes according to a scoring matrix. For example, one space is inserted into AGTGATG to result in AGTGAT-G, and three spaces are inserted into GTTAG to result in –GT--TAG. A space is denoted by a minus sign (-). The two genes are now of equal length. These two strings are aligned: AGTGAT-G -GT--TAG In this alignment, there are four matches, namely, G in the second position, T in the third, T in the sixth, and G in the eighth. Each pair of aligned characters is assigned a score according to the following scoring matrix.