Local Alignment (with Affine Gap Weights)

Years and Authors of Summarized Original Work

• 1986; Altschul, Erickson

Problem Definition

The pairwise local alignment problem is concerned with identification of a pair of similar substrings from two molecular sequences. This problem has been studied in computer science for four decades. However, most problem models were generally not biologically satisfying or interpretable before 1974. In 1974, Sellers developed a metric measure of the similarity between molecular sequences. [9] generalized this metric to include deletions and insertions of arbitrary length which represent the minimum number of mutational events required to convert one sequence into another.

Given two sequences S and T, a pairwise alignment is a way of inserting space characters ‘_’ in S and T to form sequences S^′ and T^′ respectively with the same length. There can be different alignments of two sequences. The score of an alignment is measured by a scoring metric $\updelta (x,y)$. At each position i where both x...