1. Introduction to the Pathway Tools Software David Walsh and Simon Eng bigDATA Workshop—May 29, 2010

2. Outline 1.Metabolic annotation from genomic data 2.Pathway Tools and MetaCyc facilitated genome/pathway annotation 3.Pathway/genome database (PGDB) exploration 4.Potential applications in environmental ‘omics

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4. Metabolic Annotation Workflow Assembly of DNA sequence from an organism Identification of protein-encoding genes GLIMMER FGENESB Functional annotation of genes InterProScan BLAST (COG, KEGG, etc.) Inference of metabolic pathways Microsoft Excel Illustrator Web browser Generation of a cellular/community metabolic workflow Illustrator Automated Manual Pathway Tools

5. is a software suite for working with pathway/genome databases http://bioinformatics.ai.sri.com/ptools

6. Pathway/Genome Databases (a.k.a. PGDBs) integrate genomic data with detailed functional annotations (including metabolic pathways)

7. The Three Tiers of PGDBs Tier 1 Literature derived 2 PGDBs MetaCyc and EcoCyc Tier 2 Computationally derived 15 PGDBs HumanCyc, AraCyc and other model organisms Tier 3 No curation ~400 PGDBs

8. Pathway Tools PGDBs MetaCyc EcoCyc YourCyc PGDB viewerPGDB editorPathoLogic

9. PGDB Viewer: Genome Overview

10. PGDB Viewer: Pathway Details

11. PGDB Viewer: Cellular Overview

12. MetaCyc is a continuously curated PGDB of 1400+ reference pathways from 1800+ organisms encompassing all domains of life http://www.metacyc.org

13. MetaCyc Statistics by Year Adapted from http://www.metacyc.org/release-notes.shtmlhttp://www.metacyc.org/release-notes.shtml 200120032005200720092010 Metabolic pathways445491692101014361471 Reactions421848585520657682488409 Enzymes111516183029458260566198 Genes016732931416157095952 Chemical compounds233530294817656183638572 Organisms158222601107718341861 Citations238136198599158752171322459

14. The Metabolic Hierarchy of PGDBs Metabolic pathways in PGDBs are organized in hierarchies where each pathway can have superpathways and subpathways and variants e.g., superpathway of arginine and ornithine degradation Superclasses: Degradation/Utilization/Assimilation  Amino Acids Degradation  Arginine Degradation Superpathways Subpathways: 4-aminobutyrate degradation I, arginine degradation III (arginine decarboxylase/agmatinase pathway), superpathway of arginine, putrescine, and 4-aminobutyrate degradation, superpathway of ornithine degradation, putrescine degradation II, putrescine degradation I Variants: arginine degradation II (AST pathway)

15. Novel metabolic pathways can be created at will in Pathway Tools (PGDBs are therefore dynamic)

16. PathoLogic predicts metabolic pathways in a PGDB based on reference PGDBs

17. PathoLogic reads GenBank and nucleotide FASTA files (but it also has a native file format)

18. PathoLogic infers metabolic pathways from functional annotations Product names EC numbers GO terms

19. PathoLogic applies an iterative algorithm that keeps track of candidate and undecided pathways

20. How PathoLogic Works Determine candidate and undecided pathways Prune pathways using “keep tests” and “delete tests” Keep remaining candidate and undecided pathways

21. How PathoLogic Works Iterative algorithm that tracks candidate and undecided pathways “Keep tests” – “Mostly present” pathways – Pathways with unique reactions present – Pathways with “key reactions” present “Delete tests” – “Mostly absent” pathways – Biosynthentic pathways lacking final steps – Degradative pathways missing initial steps – Pathways missing “key reactions”

22. Demonstration on two rRNA-containing fosmids of an uncultivated organism

23. Resources Pathway Tools http://bioinformatics.ai.sri.com/ptools http://bioinformatics.ai.sri.com/ptools MetaCyc http://www.metacyc.org http://www.metacyc.org