Introduction

Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation- (CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however.We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions.We have implemented our method in a software tool called Piranha. Source code and binaries, licensed under the GNU General Public License (version 3) are freely available for download from http://smithlab.usc.edu.andrewds@usc.eduSupplementary data available at Bioinformatics online.

Publications

  1. Site identification in high-throughput RNA-protein interaction data.
    Cite this
    Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD, 2012-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Philip J Uren
    Developer

    Molecular and Computational Biology, University of Southern California, United States of America

  2. Emad Bahrami-Samani
    Developer

  3. Suzanne C Burns
    Developer

  4. Mei Qiao
    Developer

  5. Fedor V Karginov
    Developer

  6. Emily Hodges
    Developer

  7. Gregory J Hannon
    Developer

  8. Jeremy R Sanford
    Developer

  9. Luiz O F Penalva
    Developer

  10. Andrew D Smith
    Investigator

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Summary
AccessionBT000081
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew D Smith