Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

BioRxiv : the Preprint Server for Biology
Hao WangCarl Kingsford

Abstract

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 naϊve mapping. Ribomap is available as open source at [http://www.cs.cmu.edu/∼ckingsf/software/ribomap][1]. [1]: http://www.cs.cmu.edu/%E2%88%BCckingsf/software/ribomap

Related Concepts

Ribosomes
RNA Splicing
Computer Software
Protein Biosynthesis
Protein Isoforms
Transcript
probe gene fragment
High-Throughput RNA Sequencing
Transcriptome

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