ArticlePloS one2013
Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
- A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR.Nature communications · 2026Article
- IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs.NAR genomics and bioinformatics · 2025Article
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.Briefings in bioinformatics · 2024Article
- CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs.BMC bioinformatics · 2022Article
- Review
- MStoCIRC: A powerful tool for downstream analysis of MS/MS data to predict translatable circRNAs.Frontiers in molecular biosciences · 2022Article
- Closing the circle: current state and perspectives of circular RNA databases.Briefings in bioinformatics · 2021Review
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA.Molecular cancer · 2020Review
- IRESpy: an XGBoost model for prediction of internal ribosome entry sites.BMC bioinformatics · 2019Article
- Computational approaches for the analysis of RNA-protein interactions: A primer for biologists.The Journal of biological chemistry · 2019Review
- Discovery ofVirus evolution · 2018Article
- Genome-wide analysis of circular RNAs in prenatal and postnatal pituitary glands of sheep.Scientific reports · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- The Evolution of LINE-1 in Vertebrates.Genome biology and evolution · 2016Article
- circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations.Scientific reports · 2016Article
- Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.Genetica · 2016Article
- IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES).Scientific reports · 2016Article
- Host MicroRNA miR-197 Plays a Negative Regulatory Role in the Enterovirus 71 Infectious Cycle by Targeting the RAN Protein.Journal of virology · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.
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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.