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Revisiting Evaluation of Multiple Sequence Alignment Methods

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Multiple Sequence Alignment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2231))

Abstract

Multiple sequence alignment is a core first step in many bioinformatics analyses, and errors in these alignments can have negative consequences for scientific studies. In this article, we review some of the recent literature evaluating multiple sequence alignment methods and identify specific challenges that arise when performing these evaluations. In particular, we discuss the different trends observed in simulation studies and when using biological benchmarks. Overall, we find that multiple sequence alignment, far from being a “solved problem,” would benefit from new attention.

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Acknowledgements

This paper was supported by NSF grant ABI-1458652 to TW. This research was also inspired by a Program on Multiple Sequence Alignment held at IPAM (Institute for Pure & Applied Mathematics, an NSF Math Institute at UCLA) in January 2015. The author wishes to thank George Chacko, whose critical comments were helpful in improving the manuscript.

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  1. Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Tandy Warnow

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  1. Tandy Warnow
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Correspondence to Tandy Warnow .

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  1. Research Institute for Microbial Disease, Osaka University, Osaka, Japan

    Kazutaka Katoh

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Warnow, T. (2021). Revisiting Evaluation of Multiple Sequence Alignment Methods. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_17

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  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

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