proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

We developed a software which detects and analyses piRNA clusters (proTRAC, probabilistic TRacking and Analysis of Clusters) based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics. We used piRNA sequences from human, macaque, mouse and rat to identify piRNA clusters in the respective species with proTRAC and compared the obtained results with piRNA cluster annotation from piRNABank and the results generated by different hitherto applied methods.proTRAC identified clusters not annotated at piRNABank and rejected annotated clusters based on the absence of important features like strand asymmetry. We further show, that proTRAC detects clusters that are passed over if a minimum number of single-copy piRNA loci are required and that proTRAC assigns more sequence reads per cluster since it does not preclude frequently mapped reads from the analysis.With proTRAC we provide a reliable tool for detection, visualization and analysis of piRNA clusters. Detected clusters are well supported by comprehensible probabilistic parameters and retain a maximum amount of information, thus overcoming the present conflict of sensitivity and specificity in piRNA cluster detection.In a wide variety of animals, mainly germline expressed small RNAs - named Piwi interacting (pi)RNAs because of their interaction with effector Piwi proteins - play an important role as guiding RNAs in safeguarding the genome from the detrimental effects of actively transposing elements [1]. Most piRNAs are encoded in strand specific genomic clusters ranging from <1kb to >100kb. Beside mono-directional clusters encoding piRNAs on only one strand, there are also bi-directional clusters whose halves encode piRNAs on opposite strands and where transcription starts in opposite directions from a centrally located promoter. In general, piRNA clusters are assumed to be transcribed into long single stranded precursors that are subject to subsequent pr