Author, as appears in the article.: Segura-Alabart, Natalia; Serratosa, Francesc; Gomez, Sergio; Fernandez, Alberto
Department: Enginyeria Informàtica i Matemàtiques Enginyeria Química
URV's Author/s: Fernández Sabater, Alberto / Gómez Jiménez, Sergio / Segura Alabart, Natàlia / Serratosa Casanelles, Francesc d'Assís
Keywords: Upgma Tie in proximity Str Ssr Microsatellite repeats Microsatellite marker Genetic diversity Dendrogram Computational biology Cluster analysis upgma tie in proximity str ssr simple sequences l. dendrogram
Abstract: Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.© The Author(s) 2022. Published by Oxford University Press.
Thematic Areas: Molecular biology Medicine (all) Mathematical & computational biology Information systems Ciências biológicas i Ciência da computação Biotechnology & applied microbiology Biochemical research methods
licence for use: https://creativecommons.org/licenses/by/3.0/es/
Author's mail: natalia.segura@urv.cat natalia.segura@urv.cat natalia.segura@urv.cat alberto.fernandez@urv.cat sergio.gomez@urv.cat francesc.serratosa@urv.cat
Author identifier: 0000-0002-1241-1646 0000-0003-1820-0062 0000-0001-6112-5913
Record's date: 2024-10-26
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://academic.oup.com/bib/article/23/5/bbac312/6652780
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Papper original source: Briefings In Bioinformatics. 23 (5): bbac312-bbac312
APA: Segura-Alabart, Natalia; Serratosa, Francesc; Gomez, Sergio; Fernandez, Alberto (2022). Nonunique UPGMA clusterings of microsatellite markers. Briefings In Bioinformatics, 23(5), bbac312-bbac312. DOI: https://doi.org/10.1093/bib/bbac312
Article's DOI: https://doi.org/10.1093/bib/bbac312
Entity: Universitat Rovira i Virgili
Journal publication year: 2022
Publication Type: Journal Publications
Repositori URV