Penjajaran Lokal Sekuen DNA Menggunakan Algoritme Smith-Waterman

Abstract

The Local Alignment of DNA sequence objective is to determine similarity between two DNA sequences. This research implements the local alignment using Smith–Waterman algorithm. The first data of Sequences from Ancylostoma duodenale (NC_003415.1) and Necator americanus (NC_003416.2), the result shows that the similarity is 84%, with 3% gaps, Second data of DNA sequence from Human papillomavirus type 134 (NC_014956.1) and Human papillomavirus type 132 (NC_014955.1), the result shows that the similarity is 62.1%, with 15.9% gaps. Third data of DNA sequence from Chaetoceros lorenzianus DNA virus (NC_015211.1) and Chaetoceros tenuissimus DNA virus (NC_014748.1), the result shows that the similarity is 53.2%, with 26.2% gaps. Last data DNA sequence from Thermoproteus tenax spherical virus 1 (NC_006556.1) and Vesicular stomatitis indiana virus (NC_001560.1), the result shows that similarity is 40.8%, with 47.6% gaps. These result shows that alignment using Smith–Waterman can result in various similarity values, depending on the length and form of sequences. The complexity of Smith-Waterman is O(mn).