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

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 https://github.com/suhrig/pingpongpro under the GPLv3 license. Supplementary information: Supplementary data are available at Bioinformatics online.