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Introduction to the Pathway Tools Software. David Walsh and Simon Eng bigDATA Workshop—May 29, 2010. Outline. Metabolic annotation from genomic data Pathway Tools and MetaCyc facilitated genome /pathway annotation Pathway/genome database (PGDB) exploration - PowerPoint PPT Presentation
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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