Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology [article]

Peter D. Karp, Suzanne M. Paley, Peter E. Midford, Markus Krummenacker, Richard Billington, Anamika Kothari, Wai Kit Ong, Pallavi Subhraveti, Ingrid M. Keseler, Ron Caspi
2020 arXiv   pre-print
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings, and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to
more » ... represent and visualize a wide range of regulatory interactions. The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit. It supports web publishing of PGDBs and provides a large number of query, visualization, and omics-data analysis tools. Scientists around the world have created more than 9,800 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms. Those PGDBs can be exchanged using a peer-to-peer database-sharing system called the PGDB Registry.
arXiv:1510.03964v4 fatcat:3plt5gcqmvg33pi6vd2mhufsda