RiboTaper

RiboTaper identifies translated regions in ribosome profiling (Ribo-seq) data by detecting the triplet periodicity of ribosomal footprints to map translation across transcriptomes.

Key Features:

• Statistical Rigor: Employs a rigorous statistical framework that capitalizes on the three-nucleotide periodicity characteristic of Ribo-seq data to enhance precision in identifying translated regions.
• Triplet Periodicity Detection: Leverages the intrinsic triplet periodicity of ribosomal footprints indicative of translating ribosomes across the transcriptome.
• De Novo ORF Identification: Identifies actively used open reading frames (ORFs) de novo within transcriptomic datasets.
• Extensive Coverage: Using deep Ribo-seq data from HEK293 cells, maps translation across more than 11,000 protein-coding genes and detects upstream ORFs and noncoding gene ORFs (ncORFs).
• Validation through Mass Spectrometry: Validation with mass spectrometry data confirms proteome coverage and supports identification of novel peptide products.

Scientific Applications:

• Transcriptome-wide Translation Mapping: Enables comprehensive mapping of translation across entire transcriptomes using Ribo-seq data.
• ORF Discovery and Annotation: Detects both known and previously unannotated ORFs for improved ORF annotation.
• Gene Expression Regulation Studies: Supports investigations into regulation from transcription through protein synthesis by identifying translated regions.
• Proteomics Integration: Provides translation evidence that can be corroborated with mass spectrometry for proteome studies.
• Noncoding RNA Translation Analysis: Identifies ribosomal signatures associated with upstream ORFs and ncORFs to study translation of noncoding RNAs.

Methodology:

Analyzes Ribo-seq data to detect triplet periodicity signals indicative of ribosome occupancy on mRNA and uses these periodicity patterns to distinguish translated regions.