ArticleBioinformatics (Oxford, England)2014
A new approach for detecting riboswitches in DNA sequences.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Functional abiotic metabolite assembly hypothesis for the early events in the origin of life.Nature communications · 2026Review
- A novel riboswitch classification based on imbalanced sequences achieved by machine learning.PLoS computational biology · 2020Article
- Development of a new oligonucleotide block location-based feature extraction (BLBFE) method for the classification of riboswitches.Molecular genetics and genomics : MGG · 2020Article
- Large-scale and significant expression from pseudogenes inMicrobial genomics · 2020Article
- Classification of Riboswitch Families Using Block Location-Based Feature Extraction (BLBFE) Method.Advanced pharmaceutical bulletin · 2020Article
- Identification and characterisation of thiamine pyrophosphate (TPP) riboswitch in Elaeis guineensis.PloS one · 2020Article
- Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy.Frontiers in bioengineering and biotechnology · 2020Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- Article
- An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles.Applied and environmental microbiology · 2018Article
- Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.PloS one · 2017Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
- RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRiboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.
resultsThe Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a 'heaviest path' problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼ 88-99% sensitivity and >99.99% specificity on 13 riboswitch families. AVAILABILITY AND IMPLEMENTATION: DRD is available at http://drd.denison.edu.
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