A Tool for Pair-Wise Alignment Algorithm

Bioinformatics is the application of computational techniques to the management and analysis of biological information. The relationship between a query sequence, commonly termed as probe and o he sequence, known as subject can be quantified and their similarity can be assessed. This similarity can be used to identify the evolutionary relationship between a newly determined sequence and a known gene family. When the degree of similarity is low, the relationship must remain competitive, until eviden e ha be ngath r d. The purpose of this research is to implement various methods for Pair-Wise alignment t chniques and d sign a to l with a good user -interface for aligning two sequences and output the score of the alignment. Thi r sea h u e the va iou pair wis alignment algorithms, like Needleman-Wunsch global alignment, Smith-Waterman algorithm to find the optimum alignment(including gaps) of two sequences. Dynamic programming methods ensure the optimal global alignment by exploring all possible alignments and choosing the best. The user will be p vided a good user-interface for giving the input sequences and opting for the required algorithm. The algorithm uses the BLOSUM50 substitution matrix for computation, and outputs the Functional mat ix(F-mat ix), Optimal Alignment and the score. The total alignment score is calculated as a function of the identity between the aligned residues and the gap penalties incurred. The input sequences can be taken from a file stored on the disk.