ArticleBriefings in bioinformatics2014
Understanding and identifying amino acid repeats.
Article in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Structural and functional insights from detailed computational analysis ofJournal of genetics · 2026Article
- High-fidelity long-read sequencing of an avian herpesvirus reveals extensive intrapopulation diversity in tandem repeat regions.PLoS pathogens · 2025Article
- AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins.Computational and structural biotechnology journal · 2025Article
- 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
- Transcriptome-wide Identification of Nine Tandem Repeat Protein Families in Roselle (Tropical life sciences research · 2024Article
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
- Disentangling the Web: An Interdisciplinary Review on the Potential and Feasibility of Spider Silk Bioproduction.ACS biomaterials science & engineering · 2024Review
- Molecular evolution of 2022 multi-country outbreak-causing monkeypox virus Clade IIb.iScience · 2024Article
- Charting Peptide Shared Sequences Between 'Diabetes-Viruses' and Human Pancreatic Proteins, Their Structural and Autoimmune Implications.Bioinformatics and biology insights · 2024Article
- Finding identical sequence repeats in multiple protein sequences: An algorithm.Journal of biosciences · 2024Article
- A robust protein language model for SARS-CoV-2 protein-protein interaction network prediction.Artificial intelligence in medicine · 2023Article
- Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins.Nucleic acids research · 2023Article
- Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Analysis of sequence diversity in Plasmodium falciparum glutamic acid-rich protein (PfGARP), an asexual blood stage vaccine candidate.Scientific reports · 2023Article
- Estimating tissue-specific peptide abundance from public RNA-Seq data.Frontiers in genetics · 2023Article
- Studying the characteristics of nanobody CDR regions based on sequence analysis in combination with 3D structures.Journal, genetic engineering & biotechnology · 2022Article
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- A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences.BMC genomics · 2021Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats.
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