MOESM2 of Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

Additional file 2. Contains the full comparison after the algorithmic and manual check of the of reactions. Full-atom mapping comparison table. With all standardised reactions, RXN file atom identifiers were extracted as an array and processed in MATLAB where they were compared if the reaction was present in the database. Comparisons were made with the following order: 1) cured reactions, 2) DREAM, 3) AutoMapper, 4) CLCA 5) MWED, and 6) ICMAP. In the curated reactions column, there are only two values, 1 or NaN if there was no file. DREAM columncould have 3 values 1 if equal than the curated reactions, 2 if are not equal and NaN if the le does not exist. AutoMapper column has 4 values, 1–3 and NaN. 1 if is equal to curated files, 2 if the mappings are equal to DREAM and 3 if they are not equal to the curated DREAM reactions and NaN if not file existed. So CLCA 1–4 and NaN, MWED 1–5 and NaN, and NaN ICMAP 1–6. If all reactions are equal, all columns 1 values obtained. With the matrix containing all the comparisons similarity of all algorithms was calculated.