Global alignment algorithms implementations

Abstract

Sequence alignment is the most basic operation in computational biology and bioinformatics. It serves as a basic for many other more complex manipulations. It is the first and most important step of homology modeling, which is based on structural similarity. However, structural similarity of two sequences is dependent on the percentage of sequence identity and number of residues aligned which is achieved by sequence alignment. In this paper, we implemented the two routes for sequence comparison, that is; the dotplot and Needleman-wunsch algorithm for global sequence alignment. Our algorithms were implemented in python programming language and were tested on Linux platform 1.60GHz, 512 MB of RAM SUSE 9.2 and 10.1 versions.

International Journal of Natural and Applied Sciences Vol. 2 (4) 2006: pp. 300-304