ArticleBMC bioinformatics2012
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 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
- DbStRiPs: Database of structural repeats in proteins.Protein science : a publication of the Protein Society · 2022Article
- Search for Highly Divergent Tandem Repeats in Amino Acid Sequences.International journal of molecular sciences · 2021Article
- Self-analysis of repeat proteins reveals evolutionarily conserved patterns.BMC bioinformatics · 2020Article
- Identification and Analysis of Long Repeats of Proteins at the Domain Level.Frontiers in bioengineering and biotechnology · 2019Article
- Secreted Cysteine-Rich Repeat Proteins "SCREPs": A Novel Multi-Domain Architecture.Frontiers in pharmacology · 2018Article
- Article
- Evolution of Protein Domain Repeats in Metazoa.Molecular biology and evolution · 2016Article
- Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.Frontiers in bioengineering and biotechnology · 2015Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats).
resultsIn this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure.
conclusionsPTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available.
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