OpenProt 2.0 builds a path to the functional characterization of alternative proteins. - Université de Lille Accéder directement au contenu
Article Dans Une Revue Nucleic Acids Research Année : 2023

OpenProt 2.0 builds a path to the functional characterization of alternative proteins.

S. Leblanc
  • Fonction : Auteur
F. Yala
  • Fonction : Auteur
N. Provencher
  • Fonction : Auteur
J. F. Lucier
  • Fonction : Auteur
M. Levesque
  • Fonction : Auteur
X. Lapointe
  • Fonction : Auteur
J. F. Jacques
  • Fonction : Auteur
A. Ouangraoua
  • Fonction : Auteur
M. S. Scott
  • Fonction : Auteur
F. M. Boisvert
  • Fonction : Auteur
M. A. Brunet
  • Fonction : Auteur
X. Roucou
  • Fonction : Auteur

Résumé

The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.
Fichier principal
Vignette du fichier
gkad1050.pdf (1.13 Mo) Télécharger le fichier
Origine Publication financée par une institution
Licence

Dates et versions

hal-04423840 , version 1 (01-02-2024)

Licence

Identifiants

Citer

S. Leblanc, F. Yala, N. Provencher, J. F. Lucier, M. Levesque, et al.. OpenProt 2.0 builds a path to the functional characterization of alternative proteins.. Nucleic Acids Research, 2023, Nucleic Acids Research, ⟨10.1093/nar/gkad1050⟩. ⟨hal-04423840⟩

Collections

UNIV-LILLE
7 Consultations
49 Téléchargements

Altmetric

Partager

Gmail Mastodon Facebook X LinkedIn More