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

  • Oier Echaniz
  • Manuel GrañaEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11486)

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.

Notes

Acknowledgments

This work has been partially supported by FEDER funds through MINECO project TIN2017-85827-P.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Grupo de Inteligencia Computacional (GIC)Universidad del País Vasco (UPV/EHU)San SebastiánSpain
  2. 2.Asociación de Ciencias de la programación Python San Sebastian (ACPYSS)San SebastiánSpain

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