ribosome profiling

ribosome profiling analyzes ribosome-protected mRNA fragments to quantify translation, map ribosome positions on mRNAs, and assess translational regulation.

Key Features:

• Data Input: Accepts BAM files as the starting format for sequence-aligned ribosome profiling reads.
• Quality Assessment: Implements functions to assess the quality of raw ribosome profiling data.
• Read Start Position Recalibration: Recalibrates read start positions to improve accuracy of ribosome footprint mapping.
• Read Counting: Counts reads across coding sequences (CDS), 3' untranslated regions (3' UTRs), and 5' UTRs.
• Translated ORF Identification: Identifies open reading frames (ORFs) that are actively translated.
• Differential Gene Expression Analysis: Performs comparisons of gene-level translation across conditions or treatments.
• Codon Decoding Rates Evaluation: Assesses local and global codon decoding rates to evaluate translational efficiency.
• Data Visualization: Produces plots for count data including pairs, log fold-change, codon frequency, and coverage assessment.
• Principal Component Analysis (PCA): Applies PCA on codon coverage to identify patterns and variation within datasets.

Scientific Applications:

• Gene Expression Assessment: Enables evaluation of gene expression at the translational level.
• Translational Regulation Studies: Supports analysis of mechanisms regulating translation and post-transcriptional control.
• Identification of Translated ORFs: Facilitates discovery of actively translated open reading frames.
• Differential Translation Analysis: Allows comparison of translational changes across experimental conditions.
• Codon Decoding Analysis: Permits examination of codon-specific decoding rates and their impact on translation dynamics.

Methodology:

Computational steps explicitly include processing BAM files, quality assessment, read start position recalibration, read counting across CDS/3' UTR/5' UTR, plotting (pairs, log fold-change, codon frequency, coverage), PCA on codon coverage, identification of translated ORFs, differential gene expression analysis, and evaluation of local and global codon decoding rates.