Introduction

: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping.Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomapcarlk@cs.cmu.eduSupplementary data are available at Bioinformatics online.

Publications

  1. Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
    Cite this
    Wang H, McManus J, Kingsford C, 2016-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Hao Wang
    Developer

  2. Joel McManus
    Developer

    Computational Biology Department, School of Computer Science and Department of Biological Sciences, United States of America

  3. Carl Kingsford
    Investigator

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Summary
AccessionBT001905
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByCarl Kingsford