HRIBO

HRIBO analyzes bacterial ribosome profiling (Ribo-seq) data to identify and prioritize unannotated open reading frames (ORFs) and small proteins (≤70 amino acids) within the bacterial translatome using ribosome-protected RNA fragments.

Key Features:

• Prokaryotic focus: Tailored explicitly for prokaryotic organisms, particularly bacteria, for Ribo-seq analysis.
• Translatome analysis: Uses ribosome-protected RNA fragments from Ribo-seq to interrogate the set of actively translated mRNAs.
• Unannotated ORF discovery: Systematically analyzes data to detect and report unannotated open reading frames (ORFs).
• Small protein detection: Targets identification of small proteins, typically those ≤70 amino acids, which are hard to detect by other methods.
• Annotation-independent ORF prediction: Generates annotation-independent ORF predictions through integration of two complementary prokaryotic-focused tools.
• Pre-processing and quality control: Implements necessary pre-processing steps and quality control measures for Ribo-seq datasets.
• Computed prioritization features: Computes multiple features to aid rapid discovery and prioritization of novel ORFs for downstream functional characterization.
• High-throughput and reproducible workflow: Provides a workflow intended for high-throughput, reproducible analysis of bacterial Ribo-seq data.

Scientific Applications:

• Bacterial translatome profiling: Characterizing actively translated mRNAs in bacteria using Ribo-seq data.
• Novel ORF and small protein discovery: Identifying previously unannotated ORFs and small proteins (≤70 amino acids) in bacterial genomes.
• Annotation refinement: Supporting refinement and expansion of bacterial genome annotations by reporting annotation-independent ORFs.
• Candidate prioritization for functional studies: Prioritizing novel ORFs for subsequent experimental functional characterization.
• Bacterial proteomics research: Contributing data and predictions relevant to studies of bacterial proteomes and microbial biology.

Methodology:

Performs Ribo-seq pre-processing and quality control, computes descriptive features for ORF prioritization, and produces annotation-independent ORF predictions by integrating two complementary prokaryotic-focused tools.