BIOTHINGS: A pipeline creation tool for PAR-CLIP sequence analysis

• Autores: Oier Echaniz, Manuel Graña Romay
• Localización: Understanding the Brain Function and Emotions: 8th International Work-Conference on the Interplay Between Natural and Artificial Computation, IWINAC 2019 Almería, Spain, June 3–7, 2019 Proceedings, Part I / José Manuel Ferrández Vicente (dir. congr.) , José Ramón Álvarez Sánchez (dir. congr.) , Félix de la Paz López (dir. congr.) , Francisco Javier Toledo Moreo (dir. congr.), Hojjat Adeli (dir. congr.), 2019, ISBN 978-3-030-19591-5, págs. 327-336
• Idioma: inglés
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• Resumen

  • Bioinformatics pipelines dealing with analysis of sequencesof 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 highthroughput 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.