Transposition of transposable elements (TEs) is the main source of genomic variation and a major driving force of genome evolution.PIWI-interacting RNAs (piRNAs) are an evolutionarily conserved mechanism for silencing TEs and other transposable elements in germline genomes of diverse metazoans including humans.Over the past several years we have developed novel bioinformatics methods to study the biogenesis and function of piRNAs.Furthermore, we recently developed a method called TEMP for detecting transposable element movements present with a wide range of frequencies in the population.We demonstrate the utility of piRNA methods and TEMP by applying them to study hybrid dysgenesis in Drosophila melanogaster, and to detect the sequence signatures of TE insertion and the phenotypic consequences of novel TE movements.