ArticleBMC bioinformatics2007
XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
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- GBSC: graph-based sequence clustering method for similar short tandem repeats in protein sequences.Bioinformatics (Oxford, England) · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
- Signatures of pathogen-driven selection and Austronesian gene flow of Papua New Guinea HLA alleles.American journal of human genetics · 2026Article
- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 2026Article
- A benchmarking framework for comparative evaluation of low-complexity region detection tools in the human proteome.Scientific reports · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Structural and functional insights from detailed computational analysis ofJournal of genetics · 2026Article
- Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences.Nucleic acids research · 2025Article
- A distinct isoform of Msp300 (nesprin) organizes the perinuclear microtubule-organizing center in adipocytes.Molecular biology of the cell · 2025Article
- A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage.Nature plants · 2024Article
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
- Short macrocyclic peptides in sponge genomes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Short tandem repeat mutations regulate gene expression in colorectal cancer.Scientific reports · 2024Article
- Article
- Comparative Structure Analysis of the Multi-Domain, Cell Envelope Proteases of Lactic Acid Bacteria.Microorganisms · 2023Article
- In-Silico Analysis Highlights the Existence in Members ofMicroorganisms · 2023Article
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Article
- A novel hypervariable variable number tandem repeat in the dopamine transporter gene (Life science alliance · 2023Article
27 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
backgroundBiological sequence repeats arranged in tandem patterns are widespread in DNA and proteins. While many software tools have been designed to detect DNA tandem repeats (TRs), useful algorithms for identifying protein TRs with varied levels of degeneracy are still needed.
resultsTo address limitations of current repeat identification methods, and to provide an efficient and flexible algorithm for the detection and analysis of TRs in protein sequences, we designed and implemented a new computational method called XSTREAM. Running time tests confirm the practicality of XSTREAM for analyses of multi-genome datasets. Each of the key capabilities of XSTREAM (e.g., merging, nesting, long-period detection, and TR architecture modeling) are demonstrated using anecdotal examples, and the utility of XSTREAM for identifying TR proteins was validated using data from a recently published paper.
conclusionWe show that XSTREAM is a practical and valuable tool for TR detection in protein and nucleotide sequences at the multi-genome scale, and an effective tool for modeling TR domains with diverse architectures and varied levels of degeneracy. Because of these useful features, XSTREAM has significant potential for the discovery of naturally-evolved modular proteins with applications for engineering novel biostructural and biomimetic materials, and identifying new vaccine and diagnostic targets.
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