ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes

Bioinformatics. 2021 Oct 11;37(19):3152-3159. doi: 10.1093/bioinformatics/btab339.

Abstract

Motivation: The annotation of small open reading frames (smORFs) of <100 codons (<300 nucleotides) is challenging due to the large number of such sequences in the genome.

Results: In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Four novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions.

Availability and implementation: Freely available on the web at https://github.com/boboppie/ORFLine.

Supplementary information: Supplementary data are available at Bioinformatics online.