README.md

Analysis of Rice phosphoprotome build

Files for re-analysis of rice phosphoproteomics datasets located in PRIDE PXD046118 using pAla FLR pipeline

https://github.com/PGB-LIV/mzidFLR

Genomic site data with SNP annotation

To generate supplementary file Gemomic_site_data_w_SNP_annotation.csv:

Uses outputs from following repros:

1. https://github.com/andrewrobertjones/rice_phospho_ptm_paper
2. https://github.com/CBFLivUni/mapping_and_enrichment

Requirements:

• RAP_DB sequence fasta
• MSU sequence fasta
• Uniprot sequence fasta

Python scripts:

Motif_seqs.py

Generates sequences used for motif analysis

Requirements:

• Output from SNP_seq_summary.py
• Database used for re-analysis results ie. Osativa_super_annotation_union_noIC4R_v2_cRAP.fasta

R scripts:

To generate manuscript figures:

• Figure 1: Overview of phosphosite counts.
• Figure 3: Motif analysis.
• Figure 4: SAAV analysis.

Located in Figs subfolder