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Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Iantorno, S; Gori, K; Goldman, N; Gil, M; Dessimoz, C; (2014) Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment. In: Multiple Sequence Alignment Methods. (pp. 59-73). Humana Press: New York, US. Green open access

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Abstract

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.

Type: Book chapter
Title: Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment
ISBN: 978-1-62703-645-0
Open access status: An open access version is available from UCL Discovery
DOI: 10.1007/978-1-62703-646-7_4
Publisher version: http://link.springer.com/protocol/10.1007%2F978-1-...
Language: English
Additional information: © Springer Science+Business Media, LLC
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/1404290
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