RiboToolkit

RiboToolkit performs comprehensive analysis and annotation of ribosome profiling (Ribo-seq) data to decode mRNA translation at codon resolution and quantify translational efficiency using ribosome-protected fragments (RPFs, typically 26–34 bp) across transcriptomes.

Key Features:

• Data Cleaning and Quality Evaluation: Performs cleaning and quality evaluation of Ribo-seq data and RPFs to support accurate downstream analyses.
• Expression Analysis Based on RPFs: Quantifies expression levels derived from ribosome-protected fragments across transcripts.
• Codon Occupancy Profiling: Profiles codon-specific ribosome occupancy to assess translation at codon resolution.
• Translation Efficiency Analysis: Computes translational efficiency metrics to compare translation relative to transcript abundance.
• Differential Translation Analysis: Identifies changes in translation between samples or experimental conditions.
• Functional Annotation: Links translated regions to functional genomic annotations for biological interpretation.
• Translation Metagene Analysis: Aggregates metagene-level translation patterns across the transcriptome to reveal global translation features.
• Identification of Actively Translated ORFs: Detects open reading frames that are actively engaged in translation.

Scientific Applications:

• Codon-resolution translation profiling: Decoding mRNA translation at codon resolution using Ribo-seq-derived RPFs (26–34 bp) across transcriptomes.
• Quantification of translational efficiency: Measuring translational efficiency of mRNAs under different biological conditions.
• Discovery of translated ORFs: Identifying actively translated open reading frames across annotated and unannotated transcripts.
• Comparative translation analysis: Detecting differential translation between samples or experimental conditions.
• Functional interpretation of the translatome: Integrating Ribo-seq signals with functional genomic annotations to interpret translational outputs.

Methodology:

Performs data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy profiling, translation efficiency and differential translation analyses, functional annotation, translation metagene analysis, and identification of actively translated ORFs.