Pathway Tools

Pathway Tools constructs and manages Pathway/Genome Databases (PGDBs) that integrate genome sequences with metabolic pathways, signaling networks, regulatory interactions, and functional annotations for biological analysis.

Key Features:

• PGDB creation and curation: Facilitates creation and curation of Pathway/Genome Databases (PGDBs) that combine genomic data with functional annotations.
• Computational inferences: Predicts metabolic pathways, identifies metabolic pathway hole fillers, and predicts operons.
• Web publishing and sharing: Supports web publishing of PGDBs and a PGDB Registry for peer-to-peer database sharing.
• Query and visualization: Provides query capabilities and visualization of pathways, networks, and annotations.
• Comparative and systems-biology analyses: Performs comparative analyses between PGDBs and systems-biology analyses including reachability analysis of metabolic networks and metabolite tracing.

Scientific Applications:

• Curated database generation: Enables development of curated PGDBs for model organisms and non-model species.
• Metabolic reconstruction and gap filling: Supports reconstruction of metabolic networks and identification of missing enzymes via pathway hole fillers.
• Regulatory and operon inference: Enables prediction of operons and integration of regulatory interactions with metabolic data.
• Comparative genomics: Facilitates comparisons across PGDBs to infer evolutionary and functional relationships.
• Network and systems analysis: Supports reachability analysis and metabolite tracing for systems-biology studies.
• Resource generation: Has been used to create over 800 PGDBs for research and database resources.

Methodology:

Computational methods explicitly include prediction of metabolic pathways, metabolic pathway hole filling, operon prediction, reachability analysis of metabolic networks, and metabolite tracing.