ArticleBioinformatics (Oxford, England)2011
A k-mer scheme to predict piRNAs and characterize locust piRNAs.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Predicting Polymerase Chain Reaction Success: Integrating theCombinatorial chemistry & high throughput screening · 2026Article
- Article
- Databases and computational methods for the identification of piRNA-related molecules: A survey.Computational and structural biotechnology journal · 2024Review
- Recent advances of PIWI-interacting RNA in cardiovascular diseases.Clinical and translational medicine · 2024Review
- Revisiting Epigenetics Fundamentals and Its Biomedical Implications.International journal of molecular sciences · 2024Review
- Regulation of insect behavior by non-coding RNAs.Science China. Life sciences · 2024Review
- LSTM4piRNA: Efficient piRNA Detection in Large-Scale Genome Databases Using a Deep Learning-Based LSTM Network.International journal of molecular sciences · 2023Article
- Exploring objective feature sets in constructing the evolution relationship of animal genome sequences.BMC genomics · 2023Article
- Review
- Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations.Journal of autoimmunity · 2023Review
- Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network.Frontiers in genetics · 2023Article
- Serum Exosome-Derived piRNAs Could Be Promising Biomarkers for HCC Diagnosis.International journal of nanomedicine · 2023Article
- HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC).BMC medical genomics · 2022Article
- Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts.EMBO reports · 2022Article
- Protein-Specific Prediction of RNA-Binding Sites Based on Information Entropy.Computational intelligence and neuroscience · 2022Article
- A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans.International journal of molecular sciences · 2021Review
- Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands.RNA biology · 2021Article
- 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
- Identification and characterization of Piwi-interacting RNAs in human placentas of preeclampsia.Scientific reports · 2021Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationIdentifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difficult and unsolved problem because piRNAs lack conservative secondary structure motifs and sequence homology in different species.
resultsIn this article, a k-mer scheme is proposed to identify piRNA sequences, relying on the training sets from non-piRNA and piRNA sequences of five model species sequenced: rat, mouse, human, fruit fly and nematode. Compared with the existing 'static' scheme based on the position-specific base usage, our novel 'dynamic' algorithm performs much better with a precision of over 90% and a sensitivity of over 60%, and the precision is verified by 5-fold cross-validation in these species. To test its validity, we use the algorithm to identify piRNAs of the migratory locust based on 603 607 deep-sequenced small RNA sequences. Totally, 87 536 piRNAs of the locust are predicted, and 4426 of them matched with existing locust transposons. The transcriptional difference between solitary and gregarious locusts was described. We also revisit the position-specific base usage of piRNAs and find the conservation in the end of piRNAs. Therefore, the method we developed can be used to identify piRNAs of non-model organisms without complete genome sequences. AVAILABILITY: The web server for implementing the algorithm and the software code are freely available to the academic community at http://59.79.168.90/piRNA/index.php.
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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.