Comparative analysis of some multiple sequence alignment tools using Gallus gallus COX1 sequences

Abstract

Multiple Sequence Alignment (MSA) is an essential method in bioinformatics for detecting conserved sequence regions and deducing evolutionary relationships. However, performance variability exists among MSA tools, and different tools yield varying results depending on the dataset. This study conducts a comparative evaluation of four widely used MSA tools: ClustalW, Clustal Omega, MUSCLE, and MAFFT. The alignment quality and processing efficiency of these tools were assessed using 40 randomly selected Gallus gallus cytochrome c oxidase subunit 1 (COX1) DNA sequences. The findings offer valuable insights into the specific contexts in which these tools may be most effective. MAFFT demonstrated a notable advantage in processing speed, while Clustal Omega and MAFFT excelled in Column Score (CS). For Total Consensus (TC) score, ClustalW and MUSCLE showed superior performance, and Clustal Omega exhibited the highest performance based on Root Mean Square Deviation (RMSD) values. No significant difference was observed between the tools in terms of the Sum-of-Pairs (SP) score. This study serves as a valuable resource for researchers seeking to optimize the use of MSA tools for their specific applications.

Keywords

• Multiple sequence alignment
• ClustalW
• Clustal Omega
• MUSCLE
• MAFFT

Supporting Institution

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Project Number

This work was not supported by any project.

Ethical Statement

The study does not require ethical approval as it does not involve experiments on humans, animals, or other living organisms.

Thanks

No acknowledgements are necessary for this study.

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