A Review about Different Multiple Sequence Alignment (MSA) Software

Daniel Park
Korea International School

Abstract

This paper presents an overview of the Multiple Sequence Alignment (MSA) methods to investigate the methodology behind them and evaluate their advantages and shortcomings. We introduce the background behind sequence alignment and study some of the multiple sequence alignment software: Clustal and MAFFT in particular. Clustal, first developed in 1988 by Des Higgins, is an extensively utilized MSA computer program during the 1990s. MAFFT was published in 2002 and is the most commonly used MSA program recently. Both programs use progressive MSA, finding the region of similarity by using pairwise alignment. We compare both of the software and appraise their effectiveness and a few potential improvements. For instance, both programs require an extensive amount of memory and use GPU(Graphics Processing Unit). Lastly, we conclude the paper with future approaches to mitigate the drawbacks and lead to the overall development of the study of bioinformatics.

Please click to read the paper.