A Quality Assessment of Protein Multiple Sequence Alignment Techniques

Multiple sequence alignment of amino acid sequences is a basic task in the field of molecular biology. MSA approaches are generally used for the 2D or 3D structure prediction of protein, evolutionary analysis, and intermolecular interactions. The quality of MSA is an important factor as it affects the results of the bioinformatics tasks. To assess the quality of MSA there are many scoring systems used. Time complexity for the exact solution of MSA is O(N)
^L
where L is the average biological sequence length and N is the total number of biological sequences in the alignment. High time complexity and lack of a reliable scoring system make this problem more complicated. In this paper we suggest the various scoring systems, along with the performance analysis of five MSA techniques, Muscle, Clustal Omega, MAFFT, ProbCons and PRANK on the account of two scoring systems, Sum-Of-Pair-Score and Total-column-Score. In order to check the effect of length of sequences on the time taken by the MSA techniques, we have also classified the sequence sets on the basis of average sequence length in the dataset and recorded time taken by the each MSA technique.