introduction to the pathway tools software david walsh and simon eng bigdata workshop—may 29, 2010
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![Page 1: Introduction to the Pathway Tools Software David Walsh and Simon Eng bigDATA Workshop—May 29, 2010](https://reader035.vdocuments.mx/reader035/viewer/2022062421/56649d485503460f94a2388c/html5/thumbnails/1.jpg)
Introduction to thePathway Tools Software
David Walsh and Simon EngbigDATA Workshop—May 29, 2010
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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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?!?!
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Metabolic Annotation Workflow
Automated
Manual
Pathway Tools
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Pathway Toolsis a software suite for working
with pathway/genome databaseshttp://bioinformatics.ai.sri.com/ptools
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Pathway/Genome Databases(a.k.a. PGDBs)
integrate genomic data withdetailed functional annotations
(including metabolic pathways)
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The Three Tiers of PGDBs
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MetaCycis a continuously curated PGDB of
1400+ reference pathways from1800+ organisms
encompassing all domains of lifehttp://www.metacyc.org
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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
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Novel metabolic pathwayscan be created at will in Pathway Tools
(PGDBs are therefore dynamic)
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PathoLogicpredicts metabolic pathways in a PGDB
based on reference PGDBs
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PathoLogicreads GenBank and nucleotide FASTA files
(but it also has a native file format)
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PathoLogicinfers metabolic pathways
from functional annotationsProduct names
EC numbersGO terms
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PathoLogicapplies an iterative algorithm
that keeps track ofcandidate and undecided pathways
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How PathoLogic Works
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Demonstrationon two rRNA-containing fosmids of
an uncultivated organism
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Resources
Pathway Tools http://bioinformatics.ai.sri.com/ptools
MetaCyc http://www.metacyc.org