TECHNOLOGY AND CODE article
Front. Hortic.
Sec. Breeding and Genetics
This article is part of the Research TopicAdvancing Biofortification: New Breeding Techniques and Agronomic Practices for Healthier ProduceView all articles
resido: An R package for exploring amino acid residue composition of peptide and protein sequences
Provisionally accepted
- U.S. Dairy Forage Research Center, Agricultural Research Service (USDA), Madison, United States
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Amino acid composition may be used in synthetic biology for fine-tuning amino acid content of plants to improve human or animal diets. One barrier to plant-based diet adoption is insufficiency of key amino acids such as methionine and lysine. Legumes, for example, are a good source of dietary protein, but lack sufficient amounts of these essential amino acids. Despite the potential utility of exploring amino acid content in proteomes or subsets of sequences, purpose-built bioinformatic tools are largely lacking. Here, we present an R package, resido, that facilitates the characterization and discovery of proteins based on amino acid content. We used resido to investigate the sulfur-containing amino acids of white lupin (Lupinus albus L.). White lupin has the potential to be a valuable component of plant-based diets, although there are some drawbacks, one being the lack of sulfur-containing amino acids in the seeds. Using resido, we identified several protein sequences that had a high percentage of sulfur amino acids; one collagen-like protein was 25% methionine. Overall, resido is a straightforward bioinformatic tool that leverages the ubiquity of R to analyze amino acid content of user-supplied peptide sequences and may be useful to efforts modulating overall amino acid content of crops for refining nutrition in animal or human diets.
Keywords: bioinformatics and computational biology, legumes (Fabaceae), Amino acids (AA), pulses, R package, Lupin (Lupinus albus L.)
Received: 14 Aug 2025; Accepted: 25 Nov 2025.
Copyright: © 2025 Stonoha-Arther and Panke-Buisse. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Christina Stonoha-Arther
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