µProteInS—a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs

• DOI: 10.1093/bioinformatics/btac115
• Publication Date: 2022-02-18T20:11:43Z
• Authors: Eduardo Vieira de...; Pedro Ferrari Dal...; Vinicius Pellisol...; Adriana Canedo; Alan Saghatelian; Pablo Machado; Luiz Augusto Basso; Cristiano Valim B...
• Keywords: 0301 basic medicine; Open Reading Frames; 03 medical and health sciences; Bacteria; Genomics; Software; Proteogenomics

AbstractSummaryGenome annotation pipelines traditionally exclude open reading frames (ORFs) shorter than 100 codons to avoid false identifications. However, studies have been showing that these may encode functional microproteins with meaningful biological roles. We developed µProteInS, a proteogenomics pipeline that combines genomics, transcriptomics and proteomics to identify novel microproteins in bacteria. Our pipeline employs a model to filter out low confidence spectra, to avoid the need for manually inspecting Mass Spectrometry data. It also overcomes the shortcomings of traditional approaches that usually exclude overlapping genes, leaderless transcripts and non-conserved sequences, characteristics that are common among small ORFs (smORFs) and hamper their identification.Availability and implementationµProteInS is implemented in Python 3.8 within an Ubuntu 20.04 environment. It is an open-source software distributed under the GNU General Public License v3, available as a command-line tool. It can be downloaded at https://github.com/Eduardo-vsouza/uproteins and either installed from source or executed as a Docker image.Supplementary informationSupplementary data are available at Bioinformatics online.