This analysis is based on a reanalysis of yeast phosphorylation data sets (PRIDE accession: PXD071918) which used alanine as a decoy to control for the false localisation rate.
This repo contains a sub-folder for each element of the downstream analysis:
01_motif_and_pathway_analysis/scripts - generation of foreground and background 15mers, motif analysis (rmotifx) and gene ontology pathway enrichment analysis (clusterProfiler).
03_disorder_analysis/scripts - processing of metapredict (V3) disorder predictions. The human analysis is based on data from Kalyuzhnyy et al., 2025.
04_AF3/scripts - generation of JSON input files for AlphaFold 3 and processing of AlphaFold models after DSSP.
05_summary/scripts - Summary figure for the yeast phosphobuild (Figure 1 in manuscript).