riboSeqR

riboSeqR analyzes ribosome profiling (ribo-seq) and matched mRNA-seq data to quantify translating ribosome positions and densities across the transcriptome.

Key Features:

• Multi-step alignment: Performs a multi-step alignment process for ribo-seq and mRNA-seq reads.
• GWIPS‑viz integration: Exports or visualizes aligned ribo-seq data as custom tracks compatible with GWIPS‑viz for comparison with published datasets.
• Quality assessment: Evaluates ribo-seq data quality and determines the strength of triplet periodicity signals.
• Meta-gene profiling: Generates meta-gene ribosome profiles to assess global translational dynamics across genes.
• Sequence impact analysis: Analyzes how mRNA sequence features influence local ribosome footprint read density.

Scientific Applications:

• Translational profiling: Maps precise locations and densities of translating ribosomes genome-wide to identify translationally active regions.
• Sequence–translation relationships: Investigates effects of mRNA sequence features on translation efficiency via local read density analyses.
• Comparative translational analysis: Compares ribosome occupancy profiles across experimental conditions or treatments.

Methodology:

Multi-step alignment of ribo-seq and mRNA-seq reads; assessment of triplet periodicity strength; generation of meta-gene ribosome profiles; analysis of correlations between mRNA sequence features and local read density; export/visualization as GWIPS‑viz custom tracks; use of published alignment workflows.