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

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

Author information

1
Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany.
2
Computational Biology Group, Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Deutschland.

Abstract

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.

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