Ribotricer

Three-nucleotide periodicity-based detection of translating ORFs from Ribo-seq

Ribotricer identifies actively translating open reading frames (ORFs) from ribosome profiling (Ribo-seq) data by quantifying the characteristic three-nucleotide periodicity of ribosome-protected mRNA fragments. It detects translation signals across annotated and short ORFs within transcriptomes.

Key Features:

• Three-Nucleotide Periodicity Analysis: Measures codon-resolved 3-nt periodicity in Ribo-seq reads to distinguish actively translating ORFs from background noise.
• Short ORF Detection: Identifies translation in short ORFs that are frequently missed by alternative methods.
• Cross-Species Applicability: Validated on datasets from Arabidopsis, Caenorhabditis elegans, Drosophila, human, mouse, rat, yeast, and zebrafish.

Scientific Applications:

• Genome-wide Translation Profiling: Enables systematic identification and evaluation of coding potential and active translation across diverse transcriptomes.

Methodology:

Ribotricer analyzes aligned Ribo-seq reads to quantify three-nucleotide periodicity within candidate ORFs, applying periodicity-based criteria to classify regions as actively translating while reducing effects of dataset heterogeneity and noise.