Peter D. Karp, Suzanne Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler and Gregory J. Phillips, “Pathway Tools Management of Pathway/Genome Data for Microbial Communities”, Frontiers in Bioinformatics. Vol. 2, April 2022, Article 869150.
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.