Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides

Loup Tran van Canh (1) , Sébastien Aubourg (1)

1 INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement

Genes encoding small secreted peptides are widely distributed among plant genomes but their detection and annotation remains challenging. The bioinformatics protocol described here aims to identify as exhaustively as possible secreted peptide precursors belonging to a family of interest. First, homology searches are performed at the protein and genome levels. Next, multiple sequence alignments and predictions of a secretion signal are used to define a set of homologous proteins sharing features of secreted peptide precursors. These protein sequences are then used as input of motif detection and profile-based tools to build representative matrices and profiles that are used iteratively as guides to scan again the proteome and genome until family completion.

Mots clés: Phytocytokine; Conserved motif; Secretion signal; Data mining; SCOOP; PIP

Domaines: Sciences du Vivant [q-bio]

Loup Tran van Canh, Sébastien Aubourg. Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides. Plant Peptide Hormones and Growth Factors, 2731, Springer US, pp.3-21, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3511-7_1⟩. ⟨hal-04394046⟩