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OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.

Marie A Brunet1,2, Mylène Brunelle1,2, Jean-François Lucier3,4

  • 1Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.

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|October 10, 2018
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Summary
This summary is machine-generated.

OpenProt is the first database supporting polycistronic eukaryotic genomes, identifying thousands of novel protein-coding open reading frames (ORFs). This advances our understanding of eukaryotic coding potential beyond traditional single coding sequence annotations.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Eukaryotic genome annotations traditionally rely on single coding sequence (CDS) per transcript, underestimating coding potential.
  • Advances in sequencing and proteomics reveal numerous unannotated open reading frames (ORFs).

Purpose of the Study:

  • To present OpenProt, the first database supporting a polycistronic model for eukaryotic genomes.
  • To comprehensively annotate all possible ORFs, including known proteins, isoforms, and novel proteins from alternative ORFs.

Main Methods:

  • Developed OpenProt database encompassing all ORFs >30 codons across 10 species.
  • Integrated evidence from protein conservation, translation, and expression data.
  • Utilized advanced algorithms for protein orthology and re-analyzed ribosome profiling and mass spectrometry datasets.

Main Results:

  • Annotated known proteins (RefProts), novel predicted isoforms (Isoforms), and novel predicted proteins from alternative ORFs (AltProts).
  • Supported annotation of thousands of predicted ORFs using evidence from 87 ribosome profiling and 114 mass spectrometry studies.
  • Provided a freely accessible web platform (www.openprot.org) with genome browser and query functionalities.

Conclusions:

  • OpenProt offers a more comprehensive view of eukaryotic genome coding potential by embracing polycistronic models.
  • The database facilitates deeper exploration of novel protein-coding regions and eukaryotic gene expression.
  • Enables researchers to access and analyze a vast repository of eukaryotic ORF data.