Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks

Tuğcan Korak; Fırat Aşır; Esin Işık; Nur Cengiz

doi:10.17776/csj.842265

EN

Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks

Abstract

Multiple sequence alignment (MSA) is a fundamental process in the studies for determination of evolutionary, structural and functional relationships of biological sequences or organisms. There are various heuristic approaches comparing more than two sequences to generate MSA. However, each tool used for MSA is not suitable for every dataset. Considering the importance of MSA in wide range of relationship studies, we were interested in comparing the performance of different MSA tools for various datasets. In this study, we applied three different MSA tools, T-Coffee, MUSCLE and M-Coffee, on several datasets, BAliBase, SABmark, DIRMBASE, ProteinBali and DNABali. It was aimed to evaluate the differences in the performance of these tools based on the stated benchmarks regarding the % consistency, sum of pairs (SP) and column scores (CS) by using Suite MSA. We also calculated the average values of these scores for each tool to examine the results in comparative perspective. Eventually, we conclude that all three tools performed their best with the datasets from ProteinBali (average % consistency: 29.6, 32.3, 29.7; SP: 0.74, 0.73, 0.74; CS with gaps: 0.27, 0.27, 0.26 for T-Coffee, MUSCLE, M-Coffee, respectively), whereas the lowest performance was obtained in datasets from DIRMBASE (average % consistency: 1.8, 1.1, 4.3; SP: 0.05, 0.04, 0.04 CS with gaps: 0.01, 0, 0.008 for T-Coffee, MUSCLE, M-Coffee, respectively)

Keywords

Multiple sequence alignment, T-Coffee, MUSCLE, M-Coffee

Thanks

The authors acknowledge Prof.Dr. Jens Allmer for his guidance in the conceptualization of this study.

References

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Details

Primary Language

English

Subjects

Structural Biology

Journal Section

Research Article

Authors

Tuğcan Korak ^*
0000-0003-4902-4022
Türkiye

Fırat Aşır
0000-0002-6384-9146
Türkiye

Esin Işık This is me
0000-0001-7635-8496
Switzerland

Nur Cengiz This is me
0000-0001-5248-3612
Germany

Publication Date

September 24, 2021

Submission Date

December 17, 2020

Acceptance Date

August 29, 2021

Published in Issue

Year 2021 Volume: 42 Number: 3

DOI

https://doi.org/10.17776/csj.842265

IZ

https://izlik.org/JA69BX93EY

APA

Korak, T., Aşır, F., Işık, E., & Cengiz, N. (2021). Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks. Cumhuriyet Science Journal, 42(3), 526-535. https://doi.org/10.17776/csj.842265

AMA

1.Korak T, Aşır F, Işık E, Cengiz N. Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks. CSJ. 2021;42(3):526-535. doi:10.17776/csj.842265

Chicago

Korak, Tuğcan, Fırat Aşır, Esin Işık, and Nur Cengiz. 2021. “Multiple Sequence Alignment Quality Comparison in T-Coffee, MUSCLE and M-Coffee Based on Different Benchmarks”. Cumhuriyet Science Journal 42 (3): 526-35. https://doi.org/10.17776/csj.842265.

EndNote

Korak T, Aşır F, Işık E, Cengiz N (September 1, 2021) Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks. Cumhuriyet Science Journal 42 3 526–535.

IEEE

[1]T. Korak, F. Aşır, E. Işık, and N. Cengiz, “Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks”, CSJ, vol. 42, no. 3, pp. 526–535, Sept. 2021, doi: 10.17776/csj.842265.

ISNAD

Korak, Tuğcan - Aşır, Fırat - Işık, Esin - Cengiz, Nur. “Multiple Sequence Alignment Quality Comparison in T-Coffee, MUSCLE and M-Coffee Based on Different Benchmarks”. Cumhuriyet Science Journal 42/3 (September 1, 2021): 526-535. https://doi.org/10.17776/csj.842265.

JAMA

1.Korak T, Aşır F, Işık E, Cengiz N. Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks. CSJ. 2021;42:526–535.

MLA

Korak, Tuğcan, et al. “Multiple Sequence Alignment Quality Comparison in T-Coffee, MUSCLE and M-Coffee Based on Different Benchmarks”. Cumhuriyet Science Journal, vol. 42, no. 3, Sept. 2021, pp. 526-35, doi:10.17776/csj.842265.

Vancouver

1.Tuğcan Korak, Fırat Aşır, Esin Işık, Nur Cengiz. Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks. CSJ. 2021 Sep. 1;42(3):526-35. doi:10.17776/csj.842265

As of 2026, Cumhuriyet Science Journal will be published in six issues per year, released in February, April, June, August, October, and December

Abstract

Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks

Abstract

Keywords

Thanks

References

Details

Primary Language

Subjects

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Authors

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Acceptance Date

Published in Issue

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