ArticleBioinformatics (Oxford, England)2010
TRStalker: an efficient heuristic for finding fuzzy tandem repeats.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 43 citations in OpenAlex.
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Advances in the discovery and analyses of human tandem repeats.Emerging topics in life sciences · 2023Review
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Use of 6 Nucleotide Length Words to Study the Complexity of Gene Sequences from Different Organisms.Entropy (Basel, Switzerland) · 2022Article
- Finding long tandem repeats in long noisy reads.Bioinformatics (Oxford, England) · 2021Article
- Article
- Self-analysis of repeat proteins reveals evolutionarily conserved patterns.BMC bioinformatics · 2020Article
- TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain.Bioinformatics (Oxford, England) · 2019Article
- Dot2dot: accurate whole-genome tandem repeats discovery.Bioinformatics (Oxford, England) · 2019Article
- A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies.Frontiers in genetics · 2018Article
- Database of Periodic DNA Regions in Major Genomes.BioMed research international · 2017Article
- Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.Genome research · 2015Article
- Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing.Bioinformatics (Oxford, England) · 2014Article
- HeteroGenome: database of genome periodicity.Database : the journal of biological databases and curation · 2014Article
- HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.Bioinformatics (Oxford, England) · 2012Article
- Fuzzy tandem repeats containing p53 response elements may define species-specific p53 target genes.PLoS genetics · 2012Article
- Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.BMC bioinformatics · 2012Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationGenomes in higher eukaryotic organisms contain a substantial amount of repeated sequences. Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity. They play an important role in several molecular regulatory mechanisms, and also in several diseases (e.g. in the group of trinucleotide repeat disorders). While for TRs with a low or medium level of divergence the current methods are rather effective, the problem of detecting TRs with higher divergence (fuzzy TRs) is still open. The detection of fuzzy TRs is propaedeutic to enriching our view of their role in regulatory mechanisms and diseases. Fuzzy TRs are also important as tools to shed light on the evolutionary history of the genome, where higher divergence correlates with more remote duplication events.
resultsWe have developed an algorithm (christened TRStalker) with the aim of detecting efficiently TRs that are hard to detect because of their inherent fuzziness, due to high levels of base substitutions, insertions and deletions. To attain this goal, we developed heuristics to solve a Steiner version of the problem for which the fuzziness is measured with respect to a motif string not necessarily present in the input string. This problem is akin to the 'generalized median string' that is known to be an NP-hard problem. Experiments with both synthetic and biological sequences demonstrate that our method performs better than current state of the art for fuzzy TRs and that the fuzzy TRs of the type we detect are indeed present in important biological sequences. AVAILABILITY: TRStalker will be integrated in the web-based TRs Discovery Service (TReaDS) at bioalgo.iit.cnr.it. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.