BIOTHINGS: A Pipeline Creation Tool for PAR-CLIP Sequence Analsys

Abstract

Bioinformatics pipelines dealing with analysis of sequences of aminoacids are tricky. It is not easy to match the input and outputs of stand-alone applications that sometimes were developed for quite different kinds of sequences. In this paper we propose a tool for the guided and safe composition of pipelines to treat a specific kind of sequences. This tool can easily extend to more general bioinformatics setting. Cross-Linking Immuno Precipitation associated to high-throughput sequencing (CLIP-seq) has been recently developed aiming to uncover the RNA-protein interaction genome-wide. Specifically PhotoActivable-Ribonucleoside-enhanced-CLIP (PAR-CLIP) has been proposed to achieve single-nucleotide resolution. A critical step in the analysis of PAR-CLIP sequences is peak calling. Specific methods propose probabilistic models based on its substitution properties, allowing for a more accurate detection of RNA-protein interaction sites. The pipeline construction tool proposed here can be used for systematic comparison of the effect of the choice of peak calling method.