ArticleNucleic acids research2018
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- DivergenteLife · 2026Article
- rbpCNN: a biophysics-informed deep learning model for predicting piRNA and mRNA interactions.Scientific reports · 2026Article
- MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.RNA (New York, N.Y.) · 2026Article
- An F2A sequence permits correct localization of a secreted and a nuclear localized reporter inmicroPublication biology · 2026Article
- piR-bmo-796514 facilitates the proliferation of exogenous DNA virus (baculovirus) by targeting the host E3 ubiquitin ligase RNF181.PLoS pathogens · 2026Article
- Engineering the auxin-inducible degron system for tunable in vivo control of organismal physiology.Nature communications · 2025Article
- A nuclear pore-anchored condensate enables germ granule organization and transgenerational epigenetic inheritance.Nature structural & molecular biology · 2025Article
- Measuring and manipulating localized translation of erm-1 in the C. elegans embryo.Development (Cambridge, England) · 2025Article
- Analysis of crosslinking sites suggestsbioRxiv : the preprint server for biology · 2025Article
- Mammalian piRNA target prediction using a hierarchical attention model.BMC bioinformatics · 2025Article
- Article
- piR-823 tale as emerging cancer-hallmark molecular marker in different cancer types: a step-toward ncRNA-precision.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- Databases and computational methods for the identification of piRNA-related molecules: A survey.Computational and structural biotechnology journal · 2024Review
- Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inRNA (New York, N.Y.) · 2023Article
- Web Services for RNA-RNA Interaction Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Review
- HIV-1 Tat and cocaine coexposure impacts piRNAs to affect astrocyte energy metabolism.Epigenomics · 2022Article
- piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting.Nucleic acids research · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Identification of piRNA disease associations using deep learning.Computational and structural biotechnology journal · 2022Article
- PiRNA pathway in the cardiovascular system: a novel regulator of cardiac differentiation, repair and regeneration.Journal of molecular medicine (Berlin, Germany) · 2021Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
pirScan is a web-based tool for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. The purpose of our tool is to allow C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable. pirScan fulfills this purpose by first enumerating the predicted piRNA-targeting sites present in an input sequence. This prediction can be exported in a tabular or graphical format. Subsequently, pirScan suggests silent mutations that can be introduced to the input sequence that would allow the modified transgene to avoid piRNA targeting. The user can customize the piRNA targeting stringency and the silent mutations that he/she wants to introduce into the sequence. The modified sequences can be re-submitted to be certain that any previously present piRNA-targeting sites are now absent and no new piRNA-targeting sites are accidentally generated. This revised sequence can finally be downloaded as a text file and/or visualized in a graphical format. pirScan is freely available for academic use at http://cosbi4.ee.ncku.edu.tw/pirScan/.
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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.