Format

Send to

Choose Destination
Nucleic Acids Res. 2019 Jan 8;47(D1):D403-D410. doi: 10.1093/nar/gky936.

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

Author information

1
Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.
2
PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France.
3
Center for Computational Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.
4
Biology Department, Université de Sherbrooke, Sherbrooke, Québec, 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, Québec, Canada.
7
Anatomy and Cell Biology Department, Université de Sherbrooke, Sherbrooke, Québec, Canada.

Abstract

Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge and on ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion of one coding sequence (CDS) per transcript, leading to a substantial underestimation of the coding potential of eukaryotes. Here, we present OpenProt, the first database fully endorsing a polycistronic model of eukaryotic genomes to date. OpenProt contains all possible ORFs longer than 30 codons across 10 species, and cumulates supporting evidence such as protein conservation, translation and expression. OpenProt annotates all known proteins (RefProts), novel predicted isoforms (Isoforms) and novel predicted proteins from alternative ORFs (AltProts). It incorporates cutting-edge algorithms to evaluate protein orthology and re-interrogate publicly available ribosome profiling and mass spectrometry datasets, supporting the annotation of thousands of predicted ORFs. The constantly growing database currently cumulates evidence from 87 ribosome profiling and 114 mass spectrometry studies from several species, tissues and cell lines. All data is freely available and downloadable from a web platform (www.openprot.org) supporting a genome browser and advanced queries for each species. Thus, OpenProt enables a more comprehensive landscape of eukaryotic genomes' coding potential.

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center