Performance Analysis of Multiple Sequence Alignment Tools

Multiple Sequence Alignment (MSA) is a process of aligning two or more sequences with the aim of finding relation between the sequences or organisms. The sequences could have mutations in ways of insertion, deletion or rearrangement of the portion of the sequences for reasons unknown over time. The sequences used for alignment could be DNA or RNA or Genes. Today, MSA is an important procedure used as an intial step in molecular biology, computational biology and bioinformatics. The outcome in these fields are, phylogenetic tree construction, protein secondary and tertiary structure analysis, and protein function prediction analysis. This paper provides a comprehensive comparative analysis of different multiple sequence alignment tools which are available today. The paper would first focus on different kinds of sequence alignment before moving to multiple sequence alignment, which then talks about the recent development in the algorithms and their techniques. The later sections would provide some of the benchmarks and data parameters used in the comparative analysis. The subsequent section would talk about the performance and the reasons for various algorithms performance and later conclude in which direction multiple sequence alignment would probably go and what we think would be ideal outcome for biologists going forward.