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Updated: Jan 6, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
Identification of Potentially Coding Small ORFs in Plant Transcriptomes
Daria Ganaeva1, Irina Lyapina1, Anna Mamaeva1
1Laboratory of Systemic Analysis of Proteins and Peptides, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
Abstract:
Small open reading frames (smORFs, <100 amino acids) are a ubiquitous feature of eukaryotic and prokaryotic genomes. However, only a fraction of these smORFs encode functional proteins, known as microproteins. Functional microproteins have been found in all three domains of life, although due to limitations in their prediction and characterization, only a few have been described in plants. Therefore, the catalogization and functional analysis of plant smORF-encoded microproteins is far from complete. In this chapter, we present a bioinformatic pipeline designed to predict and validate coding smORFs in plant transcriptomes. The workflow comprises several key steps: transcriptome assembly, prediction of potentially coding smORFs, filtration of candidates, and validation of their translation through analysis of mass-spectrometry data.
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