Introduction to thePathway Tools Software

David Walsh and Simon EngbigDATA Workshop—May 29, 2010

Outline

1. Metabolic annotation from genomic data

2. Pathway Tools and MetaCyc facilitatedgenome/pathway annotation

3. Pathway/genome database (PGDB) exploration

4. Potential applications in environmental ‘omics

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Metabolic Annotation Workflow

Automated

Manual

Pathway Tools

Pathway Toolsis a software suite for working

with pathway/genome databaseshttp://bioinformatics.ai.sri.com/ptools

Pathway/Genome Databases(a.k.a. PGDBs)

integrate genomic data withdetailed functional annotations

(including metabolic pathways)

The Three Tiers of PGDBs

MetaCycis a continuously curated PGDB of

1400+ reference pathways from1800+ organisms

encompassing all domains of lifehttp://www.metacyc.org

MetaCyc Statistics by Year

Adapted from http://www.metacyc.org/release-notes.shtml

2001 2003 2005 2007 2009 2010

Metabolic pathways 445 491 692 1010 1436 1471

Reactions 4218 4858 5520 6576 8248 8409

Enzymes 1115 1618 3029 4582 6056 6198

Genes 0 1673 2931 4161 5709 5952

Chemical compounds 2335 3029 4817 6561 8363 8572

Organisms 158 222 601 1077 1834 1861

Citations 2381 3619 8599 15875 21713 22459

Novel metabolic pathwayscan be created at will in Pathway Tools

(PGDBs are therefore dynamic)

PathoLogicpredicts metabolic pathways in a PGDB

based on reference PGDBs

PathoLogicreads GenBank and nucleotide FASTA files

(but it also has a native file format)

PathoLogicinfers metabolic pathways

from functional annotationsProduct names

EC numbersGO terms

PathoLogicapplies an iterative algorithm

that keeps track ofcandidate and undecided pathways

How PathoLogic Works

Demonstrationon two rRNA-containing fosmids of

an uncultivated organism

Resources

Pathway Tools http://bioinformatics.ai.sri.com/ptools

MetaCyc http://www.metacyc.org