Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology

TL;DR

Pathway Tools version 28.0 is a comprehensive bioinformatics software environment that integrates genome, metabolic, and regulatory informatics tools, supporting database creation, editing, sharing, and extensive data analysis for systems biology research.

Contribution

This paper introduces the latest version of Pathway Tools, enhancing its capabilities for genome, metabolic, and regulatory data analysis, and supporting a large community with over 45,000 curated organism databases.

Findings

Supports creation and editing of organism-specific databases

Enables sharing of databases via PGDB Registry

Provides extensive tools for genome, metabolic, and regulatory analysis

Abstract

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 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 45,000 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.