biostudies-literatureWang HNHGRI NIH HHS1880-2https://www.ebi.ac.uk/biostudies/studies/S-EPMC4908323biostudies-literatureUnknown32(12)<h4>Unlabelled</h4>: 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.<h4>Availability and implementation</h4>Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap<h4>Contact</h4>carlk@cs.cmu.edu<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.Bioinformatics (Oxford, England)Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.PMC4908323R21 HG006913R01 HG007104Kingsford CMcManus JWang HfalseIsoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.<h4>Unlabelled</h4>: 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.<h4>Availability and implementation</h4>Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap<h4>Contact</h4>carlk@cs.cmu.edu<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.2016-01-01T00:00:00Z2016 Jun2024-11-20T17:14:15.766Z2019-03-27T02:16:04ZS-EPMC49083232715367610.1093/bioinformatics/btw085