GraphPart: homology partitioning for biological sequence analysis

Felix Teufel, Magnús Halldór Gíslason, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Ole Winther, Henrik Nielsen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

When splitting biological sequence data for the development and testing of predictive models, it is necessary to avoid too-closely related pairs of sequences ending up in different partitions. If this is ignored, performance of prediction methods will tend to be overestimated. Several algorithms have been proposed for homology reduction, where sequences are removed until no too-closely related pairs remain. We present GraphPart, an algorithm for homology partitioning that divides the data such that closely related sequences always end up in the same partition, while keeping as many sequences as possible in the dataset. Evaluation of GraphPart on Protein, DNA and RNA datasets shows that it is capable of retaining a larger number of sequences per dataset, while providing homology separation on a par with reduction approaches.
Original languageEnglish
Article numberlqad088
JournalNAR Genomics and Bioinformatics
Volume5
Issue number4
Number of pages9
ISSN2631-9268
DOIs
Publication statusPublished - 2023

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