Openprot 2021:deeper functional annotation of the coding potential of eukaryotic genomes
| Autor: | Xavier Roucou, Jean-François Jacques, Jean-François Lucier, François-Michel Boisvert, Sebastien Leblanc, Hassan R H Al-Saedi, Maxime Levesque, Aïda Ouangraoua, Marie A. Brunet, Isabelle Fournier, Mariano Avino, Frédéric Grenier, Noé Guilloy, Michelle S. Scott, Michel Salzet |
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| Přispěvatelé: | INSERM, Université de Lille, Faculté de médecine et des sciences de la santé [Sherbrooke] [UdeS], Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U1192, 540998|||PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Faculté des sciences [Sherbrooke] [UdeS], PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP)-Université de Sherbrooke (UdeS)-Université Laval [Québec] (ULaval)-McGill University = Université McGill [Montréal, Canada]-University of Ottawa [Ottawa]-Université du Québec à Trois-Rivières (UQTR)-Université de Montréal (UdeM)-TransBiotech, Lévis-Concordia University [Montreal]-Université du Québec à Montréal = University of Québec in Montréal (UQAM), Faculté de médecine et des sciences de la santé [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U 1192 (PRISM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
AcademicSubjects/SCI00010
[SDV]Life Sciences [q-bio] Computational biology Biology Genome Mass Spectrometry 03 medical and health sciences Annotation Open Reading Frames User-Computer Interface 0302 clinical medicine Genetics RefSeq Ensembl Protein Isoforms Database Issue Ribosome profiling Databases Protein 030304 developmental biology Proteogenomics 0303 health sciences Eukaryota Molecular Sequence Annotation Open reading frame Ribosomes 030217 neurology & neurosurgery |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, 2020, Nucleic Acids Research, 49 (D1), pp.D380-D388. ⟨10.1093/nar/gkaa1036⟩ |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkaa1036⟩ |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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