ArticleBMC bioinformatics2016
RNA motif search with data-driven element ordering.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation.Cell reports · 2026Article
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Robo-Therm, a pipeline to RNA thermometer discovery and validation.RNA (New York, N.Y.) · 2024Article
- Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages.Nature communications · 2024Article
- Characterization of a FourU RNA Thermometer in the 5' Untranslated Region of Autolysin GeneBiochemistry · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundIn this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms.
resultsWe have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools.
conclusionsWe have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.