IpiRId: Integrative approach for piRNA prediction using genomic and epigenomic data

Abstract

Many computational tools have been proposed during the two last decades for predicting piRNAs, which are molecules with important role in post-transcriptional gene regulation. However, these tools are mostly based on only one feature that is generally related to the sequence. Discoveries in the domain of piRNAs are still in their beginning stages, and recent publications have shown many new properties. Here, we propose an integrative approach for piRNA prediction in which several types of genomic and epigenomic properties that can be used to characterize these molecules are examined. We reviewed and extracted a large number of piRNA features from the literature that have been observed experimentally in several species. These features are represented by different kernels, in a Multiple Kernel Learning based approach, implemented within an object-oriented framework. The obtained tool, called IpiRId, shows prediction results that attain more than 90% of accuracy on different tested species (human, mouse and fly), outperforming all existing tools. Besides, our method makes it possible to study the validity of each given feature in a given species. Finally, the developed tool is modular and easily extensible, and can be adapted for predicting other types of ncRNAs. The IpiRId software and the user-friendly web-based server of our tool are now freely available to academic users at: https: //evryrna.ibisc.univ-evry.fr/evryrna/.