ArticleBMC bioinformatics2014
Prediction of piRNAs using transposon interaction and a support vector machine.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
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- MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.RNA (New York, N.Y.) · 2026Article
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- Databases and computational methods for the identification of piRNA-related molecules: A survey.Computational and structural biotechnology journal · 2024Review
- Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations.Journal of autoimmunity · 2023Review
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- A combined miRNA-piRNA signature in the serum and urine of rabbits infected with Toxoplasma gondii oocysts.Parasites & vectors · 2022Article
- First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome.BMC biology · 2022Article
- Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus.BMC genomics · 2022Article
- The repertoire of testicular extracellular vesicle cargoes and their involvement in inter-compartmental communication associated with spermatogenesis.BMC biology · 2022Article
- De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome.Environmental toxicology and chemistry · 2022Article
- A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans.International journal of molecular sciences · 2021Review
- Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements.Biology · 2021Review
- Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs.International journal of molecular sciences · 2021Review
- AASRA: an anchor alignment-based small RNA annotation pipeline†.Biology of reproduction · 2021Article
- The biogenesis and biological function of PIWI-interacting RNA in cancer.Journal of hematology & oncology · 2021Review
- RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.BMC bioinformatics · 2021Article
- Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells.International journal of molecular sciences · 2021Article
- Characterization of microRNA Profiles inFrontiers in veterinary science · 2021Article
- Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders.Frontiers in endocrinology · 2021Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPiwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction of piRNAs remains a significant challenge.
resultsWe developed a program for piRNA annotation (Piano) using piRNA-transposon interaction information. We downloaded 13,848 Drosophila piRNAs and 261,500 Drosophila transposons. The piRNAs were aligned to transposons with a maximum of three mismatches. Then, piRNA-transposon interactions were predicted by RNAplex. Triplet elements combining structure and sequence information were extracted from piRNA-transposon matching/pairing duplexes. A support vector machine (SVM) was used on these triplet elements to classify real and pseudo piRNAs, achieving 95.3 ± 0.33% accuracy and 96.0 ± 0.5% sensitivity. The SVM classifier can be used to correctly predict human, mouse and rat piRNAs, with overall accuracy of 90.6%. We used Piano to predict piRNAs for the rice stem borer, Chilo suppressalis, an important rice insect pest that causes huge yield loss. As a result, 82,639 piRNAs were predicted in C. suppressalis.
conclusionsPiano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions. Piano is freely available to the academic community at http://ento.njau.edu.cn/Piano.html .
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