Published title is Resido: an R package for exploring amino acid residue composition of peptide and protein sequences

Authors: Arther, Christina; Panke-Buisse, Kevin

Submitted to: Frontiers in Horticulture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2025
Publication Date: 12/11/2025
Citation: Arther, C.M., Panke-Buisse, K. 2025. Published title is Resido: an R package for exploring amino acid residue composition of peptide and protein sequences. Frontiers in Horticulture. https://doi.org/10.3389/fhort.2025.1686134.
DOI: https://doi.org/10.3389/fhort.2025.1686134

Interpretive Summary: Bioinformatics can be an important tool for identifying genetic targets in synthetic biology. One hurdle in plant-based diets for both animals and humans is the lack of certain 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. Synthetic biology techniques may be used to increase the levels of one or both of these amino acids in order to improve the nutritional value of legume crops. To this end, we have developed a straightforward bioinformatic tool, called resido, that identifies, quantifies, and sorts amino acids of interest in protein sequences using R statistical software. This package takes a user-supplied file containing protein and/or peptide sequences and has several output options including visual outputs that show amino acid frequencies over the protein sequence and compares amino acids between multiple protein sequences. This tool may help identify gene targets in crops that can be overexpressed in order to increase levels of dietary amino acids.

Technical Abstract: Amino acid composition may be used in synthetic biology for fine-tuning amino acid content of plants for improving diets of humans or animals. For example, many legumes lack sufficient levels of lysine and methionine to be nutritionally complete. Increasing the amounts of these two amino acids through genetic modification has the potential to improve them for use in human and animal diets. Despite the potential utility of exploring amino acid content in proteomes or subsets of sequences, bioinformatics tools for this purpose are largely lacking. Here, we present an R package, resido, that facilitates the characterization and discovery of proteins based on amino acid content. resido accepts a FASTA file of one or more amino acid sequences and offers various output options. The default output is a dataframe or CSV file that reports either the total number of amino acids (or amino acids groups) of interest per sequence, or the percent amino acid per sequence. There are also visual output options that illustrate amino acid frequency of peptide sequences as well as multi-protein heat map comparisons of amino acids. Overall, resido is a straightforward bioinformatic tool to analyze amino acid content of user-supplied peptide sequences.