Position-Residue Specific Dynamic Gap Penalty Scoring Strategy for Multiple Sequence Alignment

Abstract

Multiple Sequence Alignment (MSA) is a basic tool for biological sequence analysis and also a crucial step utilized by biologists to analyze phylogentic, gene regulations, homology marker, drug discovery, and predicting the protein structure and its functions. Effective Alignment of multiple sequences having biologic relevance is still an open problem. Accuracy of MSA is highly dependent on the scoring function, which aligns a given residue to its appropriate position during alignment. Scoring function has three possible cases to score a pair of residues: i) a residue with same residue, ii) a residue with different residue and iii) a residue with gap. A number of biological meaningful approaches are developed for the first two cases. However, for the third case, most of the approaches follow the default score for gap penalty, which is provided as an input by an expert. In this study, we propose a new, biologically relevant, and position-residue specific dynamic scoring approach for gap penalty. Position-Residue Specific Dynamic Gap Penalty (PRSDGP) scoring function is tested on the BAliBASE benchmark dataset. The proposed PRSDGP scoring approach is compared with the CLUSTAL O program and Quality metric improvement ranges from 46.2% to 81.5%.