PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data

Bioinformatics. 2019 Jan 15;35(2):335-336. doi: 10.1093/bioinformatics/bty578.


Summary: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs which guide endonucleases to mRNAs of actively transcribed transposons in order to prevent their translation. The resulting mRNA fragments induce a positive feedback loop (the 'ping-pong cycle'), which reinforces piRNA production and hence the transposon-silencing effect. PingPongPro is a command-line tool to scan small RNA-Seq data for signs of ping-pong cycle activity. It implements a novel algorithm that combines empirical probabilities in a multi-factor model to accurately identify transposons which are suppressed through the ping-pong cycle.

Availability and implementation: Source code, a user manual, and binaries for Microsoft Windows and Linux are available at under the GPLv3 license.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Computational Biology
  • DNA Transposable Elements*
  • RNA, Messenger
  • RNA, Small Interfering / genetics*
  • Sequence Analysis, RNA*
  • Software*


  • DNA Transposable Elements
  • RNA, Messenger
  • RNA, Small Interfering