Pairewise Alignment

Two sequences are homologous if they diverged from a common ancestor. Since homology implies biological similarity, homologous sequences are often identified if the similarity score of two sequences is greater than a threshold value. 

The goal of sequence alignment is to estimate insertion/deletion in DNA or protein sequences by maximizing similarity scores. There are two types of alignment – global alignment and local alignment. Global alignment finds the best alignment for the entire sequences. In contrast, local alignment finds local regions with high level of similarity.