Code and derived data for: Reading amino acid composition from seaweed genomes: abundance-weighted predicted proteomes against measured profiles

This record holds the analysis scripts, derived tables, Online Resources 1 to 4 and Figures 1 to 6 for the article "Reading amino acid composition from seaweed genomes: abundance-weighted predicted proteomes against measured profiles", submitted to the Journal of Applied Phycology. The study predicts the amino acid composition of 10 seaweeds from genome-based protein sets weighted by public RNA-seq transcript abundance, with a plastid-encoded protein term from lineage proteomics. The predictions are compared with filtered measured hydrolysate profiles from a published compilation. The scripts cover target building, salmon quantification of the first 4,000,000 read pairs of 52 public RNA-seq runs, the 5 composition estimators, profile filters, agreement statistics, predicted amino acid scores, sensitivity checks, an assembly pilot in Saccharina latissima, the country map and the manuscript figures. The folder derived/results_fp holds the full-precision tables behind the numbers in the article, and the folder derived/results holds stage tables and salmon quant.sf outputs. A README file lists every folder, the order of the scripts, the software versions and the steps to rerun the analysis. All raw inputs are public and are not redistributed here. These inputs are the Angell et al. (2015) amino acid compilation (DOI 10.4225/28/55776D6F45871), PRIDE proteomics projects PXD069102, PXD011219 and PXD052629, 10 NCBI genome assemblies with organelle genomes, and RNA-seq runs from 15 BioProjects listed in Online Resource 1. Data and tables are released under CC BY 4.0, and the code is released under the MIT License. Version 1.1 replaces the figure files with 8-bit RGB TIFF files at 600 dpi and a new Figure 3 layout, with no change to the data.