ArticleGenome research2013
Structure-based whole-genome realignment reveals many novel noncoding RNAs.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis.PloS one · 2024Article
- Conserved long-range base pairings are associated with pre-mRNA processing of human genes.Nature communications · 2021Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology.Non-coding RNA · 2019Review
- Identification and characterization of novel conserved RNA structures in Drosophila.BMC genomics · 2018Article
- Review
- Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease.Scientific reports · 2017Article
- Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.BMC genomics · 2017Article
- RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.Bioinformatics (Oxford, England) · 2017Article
- Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals.PLoS genetics · 2015Article
- Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.BMC genomics · 2015Article
- ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs.BMC bioinformatics · 2014Article
- IRBIS: a systematic search for conserved complementarity.RNA (New York, N.Y.) · 2014Article
- Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila.RNA (New York, N.Y.) · 2014Article
- Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Biophysical journal · 2014Article
- Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites.Nucleic acids research · 2014Article
- Article
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.Annual review of biophysics · 2014Review
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.Algorithms for molecular biology : AMB · 2013Article
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3 authors.
Funding
Abstract
Recent genome-wide computational screens that search for conservation of RNA secondary structure in whole-genome alignments (WGAs) have predicted thousands of structural noncoding RNAs (ncRNAs). The sensitivity of such approaches, however, is limited, due to their reliance on sequence-based whole-genome aligners, which regularly misalign structural ncRNAs. This suggests that many more structural ncRNAs may remain undetected. Structure-based alignment, which could increase the sensitivity, has been prohibitive for genome-wide screens due to its extreme computational costs. Breaking this barrier, we present the pipeline REAPR (RE-Alignment for Prediction of structural ncRNA), which efficiently realigns whole genomes based on RNA sequence and structure, thus allowing us to boost the performance of de novo ncRNA predictors, such as RNAz. Key to the pipeline's efficiency is the development of a novel banding technique for multiple RNA alignment. REAPR significantly outperforms the widely used predictors RNAz and EvoFold in genome-wide screens; in direct comparison to the most recent RNAz screen on D. melanogaster, REAPR predicts twice as many high-confidence ncRNA candidates. Moreover, modENCODE RNA-seq experiments confirm a substantial number of its predictions as transcripts. REAPR's advancement of de novo structural characterization of ncRNAs complements the identification of transcripts from rapidly accumulating RNA-seq data.
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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.