letterNature BiotechnologyJul 1, 2022HYBRID OA

Standardized annotation of translated open reading frames

JMJonathan M. MudgeJRJorge Ruiz‐OreraJRJohn R. PrensnerMAMarie A. BrunetFCFerriol Calvet

European Bioinformatics Institute · Max Delbrück Center · +29 more institutions

PubMed
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Abstract

Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs because of uncertainties about their experimental reproducibility and physiological roles. Yet, it is clear that certain ‘Ribo-seq ORFs’ make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain…

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Topics & keywords

Topics
Keywords
  • Annotation
  • Open reading frame
  • Reading (process)
  • Computer science
  • Information retrieval
  • Computational biology
  • Natural language processing
  • Biology
UN Sustainable Development Goals
  • Quality Education
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