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.
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This work has been partially supported by FEDER funds through MINECO project TIN2017-85827-P.
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Echaniz, O., Graña, M. (2019). BIOTHINGS: A Pipeline Creation Tool for PAR-CLIP Sequence Analsys. In: Ferrández Vicente, J., Álvarez-Sánchez, J., de la Paz López, F., Toledo Moreo, J., Adeli, H. (eds) Understanding the Brain Function and Emotions. IWINAC 2019. Lecture Notes in Computer Science(), vol 11486. Springer, Cham. https://doi.org/10.1007/978-3-030-19591-5_34
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DOI: https://doi.org/10.1007/978-3-030-19591-5_34
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