OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes

Author:

Brunet Marie A12,Lucier Jean-François34,Levesque Maxime34,Leblanc Sébastien12,Jacques Jean-Francois12,Al-Saedi Hassan R H1,Guilloy Noé12,Grenier Frederic34ORCID,Avino Mariano1,Fournier Isabelle5,Salzet Michel5,Ouangraoua Aïda6ORCID,Scott Michelle S1ORCID,Boisvert François-Michel7,Roucou Xavier12ORCID

Affiliation:

1. Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada

2. PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada

3. Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada

4. Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada

5. INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France

6. Informatics Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada

7. Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada

Abstract

Abstract OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one’s bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.

Funder

Canada Research Chairs

Canadian Institutes of Health Research

Publisher

Oxford University Press (OUP)

Subject

Genetics

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