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ULTRA: A Model Based Tool to Detect Tandem Repeats.
Article in ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Kinetically Trapped Ligand Binding in DNA Tandem Repeats.Biochemistry · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.Genome biology and evolution · 2025Article
- Short tandem repeats delineate gene bodies across eukaryotes.Nature communications · 2024Article
- SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies.Briefings in bioinformatics · 2024Article
- The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice.Nature communications · 2024Article
- ULTRA-Effective Labeling of Repetitive Genomic Sequence.bioRxiv : the preprint server for biology · 2024Article
- Article
- nail: software for high-speed, high-sensitivity protein sequence annotation.bioRxiv : the preprint server for biology · 2024Article
- WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences.Bioinformatics advances · 2024Article
- ULTRA-effective labeling of tandem repeats in genomic sequence.Bioinformatics advances · 2024Article
- A chromosomal reference genome sequence for the malaria mosquito,Wellcome open research · 2024Article
- A chromosomal reference genome sequence for the malaria mosquito,Wellcome open research · 2024Article
- Chromosomal reference genome sequences for the malaria mosquito,Wellcome open research · 2024Article
- A chromosomal reference genome sequence for the malaria mosquito,Wellcome open research · 2024Article
- Advances in the discovery and analyses of human tandem repeats.Emerging topics in life sciences · 2023Review
- Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.Nature genetics · 2023Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras.Molecular biology and evolution · 2022Article
- Methodologies for theGenes · 2022Review
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2 authors.
Funding
Abstract
In biological sequences, tandem repeats consist of tens to hundreds of residues of a repeated pattern, such as atgatgatgatgatg ('atg' repeated), often the result of replication slippage. Over time, these repeats decay so that the original sharp pattern of repetition is somewhat obscured, but even degenerate repeats pose a problem for sequence annotation: when two sequences both contain shared patterns of similar repetition, the result can be a false signal of sequence homology. We describe an implementation of a new hidden Markov model for detecting tandem repeats that shows substantially improved sensitivity to labeling decayed repetitive regions, presents low and reliable false annotation rates across a wide range of sequence composition, and produces scores that follow a stable distribution. On typical genomic sequence, the time and memory requirements of the resulting tool (
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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.