RiboA

A (Ribo-Seq A-site Identifier): Integer programming-based A-site detection for Ribo-Seq

RiboA identifies ribosome A-site locations on ribosome-protected mRNA fragments from ribosome profiling (Ribo-Seq) data. It determines the codon position where translation occurs, enabling accurate mapping of codons translated into amino acids and improving signal-to-noise ratios for translational analyses.

Key Features:

• Integer Programming-Based A-site Identification: Applies an Integer Programming algorithm to assign A-site positions, constrained by the biological assumption that the A-site of actively translating ribosomes lies between the second codon and the stop codon of coding sequences (CDS).
• Fragment Length and CDS Coverage Support: Analyzes diverse ribosome-protected mRNA fragment sizes within and around coding sequences to accommodate heterogeneous Ribo-Seq datasets.
• A-site Read Density Profiling: Generates A-site read density profiles for quantitative assessment of ribosome occupancy.

Scientific Applications:

• Translational Dynamics Analysis: Enables transcriptome-wide investigation of translational efficiency, codon-level ribosome occupancy, and regulatory mechanisms influencing protein synthesis.

Methodology:

RiboA formulates A-site assignment as an Integer Programming optimization problem, incorporating biological constraints that restrict valid A-site positions to the region between the second codon and the stop codon of annotated coding sequences. Optimal offsets are inferred for ribosome-protected fragment lengths to maximize biologically consistent A-site positioning.