Sequence alignment serves as the basis for comparing two sequences. The score obtained from the comparison of two sequences, the query and the candidate sequence in the database, is in turn, used to retrieve the candidate sequences that are related to the query as evidenced by the value of their similarity score. While performing real-time searches, the sheer size of the database often precludes the applicability of obvious and direct approaches. It necessitates the development of algorithms that can yield approximate scores in a reasonable turnaround time. Consequently, the practical search algorithms are not guaranteed to produce the best or the optimal matches. Rather, offer a high probability that the matches returned will be true matches of the query and the retrieved database sequence. Often, a p-value is associated with the retrieved sequence that indicates the probability that the match detected by the retrieval procedure could have occurred simply by chance. Alternatively, an Expect or an E-value may be returned by such a procedure indicative of the probability with which the reported score can be expected simply by chance.