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

Year 2024, Volume: 37 Issue: 3, 143 - 146, 06.12.2024

Kemal Eskioglu , Berkant Ismail Yildiz , Demir Ozdemir

https://doi.org/10.29136/mediterranean.1551310

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

Project Number

This work was not supported by any project.

References

• Aniba MR, Poch O, Thompson JD (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Research 38: 7353-7363.
• Chowdhury B, Garai G (2017) A review on multiple sequence alignment from the perspective of genetic algorithm. Genomics 109: 419-431.
• Ferrer‐Costa C, Orozco M, de la Cruz X (2005) Use of bioinformatics tools for the annotation of disease‐associated mutations in animal models. Proteins: Structure, Function, and Bioinformatics 61: 878-887.
• Katoh K, Misawa K, Kuma KI, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066.
• Katoh K, Kuma KI, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33(2): 511-518.
• Levasseur A, Pontarotti P, Poch O, Thompson JD (2008) Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evolutionary Bioinformatics 4: EBO-S597.
• Mohamed EM, Mousa HM, Keshk AE (2018) Comparative analysis of multiple sequence alignment tools. International Journal of Information Technology and Computer Science 10: 24-30.
• Nuin PA, Wang Z, Tillier ER (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7: 1-18.
• Pais FSM, Ruy PDC, Oliveira G, Coimbra RS (2014) Assessing the efficiency of multiple sequence alignment programs. Algorithms for Molecular Biology 9: 1-8.
• Park D, Park SH, Ban YW, Kim YS, Park KC, Kim NS, Kim Choi IY (2017) A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data. BMC Biotechnology 17: 1-8.
• Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, Shoaib M (2014) Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evolutionary Bioinformatics, 10: EBO-S19199.
• Prykhozhij SV, Rajan V, Gaston D, Berman JN (2015) CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PloS one 10: e0119372.
• Sievers F, Higgins DG (2018) Clustal Omega for making accurate alignments of many protein sequences. Protein Science 27: 135-145.
• Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
• Thompson JD, Linard B, Lecompte O, Poch O (2011) A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PloS one, 6: e18093.