OpenProt

OpenProt annotates the eukaryotic proteome using a polycistronic genome annotation model to identify RefProts, novel isoforms, and alternative proteins (altProts), including open reading frames (ORFs) in untranslated regions, ORFs overlapping known coding sequences, and ORFs within non-coding RNAs.

Key Features:

• Polycistronic annotation model: Implements a polycistronic genome annotation model for eukaryotic transcriptomes.
• Comprehensive annotation: Annotates RefProts, novel isoforms, and altProts across transcripts.
• Alternative ORF detection: Identifies ORFs in untranslated regions (UTRs), ORFs overlapping known coding sequences, and ORFs within annotated non-coding RNAs.
• Multi-omic evidence integration: Integrates mass spectrometry and ribosome profiling evidence to support protein annotations.
• Re-analysis of datasets: Re-analyzes 114 mass spectrometry datasets and 87 ribosome profiling datasets to compile experimental evidence.
• Protein homology assessment: Performs protein homology assessments to infer relatedness to known proteins.
• Functional domain prediction: Predicts functional domains for annotated proteins.
• Multi-species coverage: Provides proteogenomic annotation across an exhaustive transcriptome spanning ten species.

Scientific Applications:

• Expanded proteome annotation: Extends annotated proteomes to include previously unannotated altProts and novel isoforms.
• Validation of translated ORFs: Provides experimental support for translation of ORFs located in UTRs, overlapping coding sequences, or non-coding RNAs via mass spectrometry and ribosome profiling reanalysis.
• Functional inference: Enables functional inference for newly annotated proteins through homology assessment and domain prediction.
• Cross-species proteogenomics: Supports proteogenomic analyses across ten species to study proteome complexity and conservation.

Methodology:

Adopts a polycistronic annotation model and annotates RefProts, novel isoforms, and altProts; integrates mass spectrometry and ribosome profiling evidence with protein homology assessments and functional domain prediction; and re-analyzes 114 mass spectrometry datasets and 87 ribosome profiling datasets across an exhaustive transcriptome spanning ten species.