sORFs

sORFs catalogs small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq) to enable discovery and proteomic validation of micropeptides and translated sORFs.

Key Features:

• Extensive dataset: Hosts over 263,354 sORFs with ribosome occupancy across six species derived from more than 78 RIBO-seq datasets, including HCT116 (human), E14_mESC (mouse), S2 (Drosophila), zebrafish, rat, and Caenorhabditis elegans.
• Advanced detection pipeline: Detects sORFs in datasets containing solely elongating ribosome profiling data, removing the previous requirement for initiating RIBO-seq data.
• Noise filtering algorithm: Implements a noise filtering algorithm that distinguishes true ribosomal activity from simulated noise to reduce false positives in sORF identification.
• Sequence similarity assessment: Executes an internal BLAST pipeline to evaluate sequence similarity among sORFs for comparative and functional inference.
• Proteomics integration: Integrates a full PRIDE-ReSpin pipeline to reprocess public MS-based proteomics datasets from the PRIDE database for identification of translation events and micropeptide validation.
• Visualization tools: Provides inspection of annotated spectra using the Lorikeet MS/MS viewer for manual review of peptide-spectrum matches.

Scientific Applications:

• Micropeptide discovery: Supports identification and cataloging of micropeptides encoded by sORFs using RIBO-seq evidence.
• Cross-species comparison: Enables comparative sequence analyses and conservation studies among included species using the internal BLAST pipeline.
• Proteomic validation: Facilitates validation of translation events and peptide identification by reprocessing PRIDE MS datasets with PRIDE-ReSpin and inspecting spectra.
• Gene expression and peptide function studies: Aids investigations into gene expression regulation and the functional characterization of peptides encoded by sORFs.

Methodology:

Processes ribosome profiling (RIBO-seq) data using a detection pipeline for elongating RIBO-seq datasets, applies a noise filtering algorithm, performs sequence similarity searches with BLAST, reprocesses PRIDE MS datasets via the PRIDE-ReSpin pipeline, and presents annotated spectra for inspection in the Lorikeet MS/MS viewer.