PirScan: A webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans

Wei Sheng Wu, Wei Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng Chi Lee

Research output: Contribution to journalArticle

9 Citations (Scopus)

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 allowC. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has renderedmany 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.

Original languageEnglish
Pages (from-to)W43-W48
JournalNucleic acids research
Volume46
Issue numberW1
DOIs
Publication statusPublished - 2018 Jul 2

All Science Journal Classification (ASJC) codes

  • Genetics

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