title: Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
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 naïve mapping.
  
  
  
  Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap
  
  
  
  carlk@cs.cmu.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Biology Department, School of Computer Science and.
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.affiliation: Computational Biology Department, School of Computer Science and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: McManus
authors.affiliation: Computational Biology Department, School of Computer Science and.
authors.forename: Carl
authors.initials: C
authors.lastname: Kingsford
mesh_terms: D017398:Alternative Splicing; D059014:High-Throughput Nucleotide Sequencing; D020033:Protein Isoforms; D012270:Ribosomes; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D020033:Protein Isoforms