ArticleBMC bioinformatics2020
Self-analysis of repeat proteins reveals evolutionarily conserved patterns.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Distinct repeat architecture landscapes in the proteomes of protozoan parasites.NAR genomics and bioinformatics · 2026Article
- Discovery and Analysis of Repeat and Low-Complexity Architectures in Proteins and Their Conserved Evolutionary Relationships Using Self-Homology Dot Plots.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evolutionary model of repeat insertions in Ataxin-3 traces the origin of the polyglutamine stretch to an ancestral ubiquitin binding module.Protein science : a publication of the Protein Society · 2024Article
- Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins.Biomolecules · 2024Article
- The Repeating, Modular Architecture of the HtrA Proteases.Biomolecules · 2022Article
- RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundProtein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution. We noted that the patterns derived from traditional "dot plot" protein sequence self-similarity analysis tended to be conserved in sets of related repeat proteins and this conservation could be quantitated using a Jaccard metric.
resultsComparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information. Analysis of the UniRef90 database suggested that 16.9% of all known proteins could be classified as repeat proteins. These 13.3 million putative repeat protein chains were clustered and a significant amount (82.9%) of clusters containing between 5 and 200 members were of a single functional type.
conclusionsDot plot analysis of repeat proteins attempts to obviate issues that arise due to the sequence degeneracy of repeat proteins. These results show that this kind of analysis can efficiently be applied to analyze repeat proteins on a large scale.
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