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The pathway tools pathway prediction algorithm.

Karp PD, Latendresse M, Caspi R - Stand Genomic Sci (2011)

Bottom Line: Both phases draw on the MetaCyc database of metabolic reactions and pathways.MetaCyc contains two data fields to support pathway inference: the expected taxonomic range of each pathway, and a list of key reactions for pathways.These fields have significantly increased the predictive accuracy of PathoLogic.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Group, SRI International 333 Ravenswood Ave, EK207, Menlo Park, CA 94025.

ABSTRACT
The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. The algorithm consists of two phases. The reactome inference phase infers the reactions catalyzed by the organism from the set of enzymes present in the annotated genome. The pathway inference phase infers the metabolic pathways present in the organism from the reactions catalyzed by the organism. Both phases draw on the MetaCyc database of metabolic reactions and pathways. MetaCyc contains two data fields to support pathway inference: the expected taxonomic range of each pathway, and a list of key reactions for pathways. These fields have significantly increased the predictive accuracy of PathoLogic.

No MeSH data available.


Example pathway illustrating how MetaCyc curators sometimes split pathways into smaller evolutionarily conserved units.
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f1: Example pathway illustrating how MetaCyc curators sometimes split pathways into smaller evolutionarily conserved units.

Mentions: The MetaCyc metabolic database is the reference pathway database used by PathoLogic for pathway prediction [Figure 1]. Version 14.6 (released in November 2010) of MetaCyc contains 1,583 base metabolic pathways and 263 superpathways.


The pathway tools pathway prediction algorithm.

Karp PD, Latendresse M, Caspi R - Stand Genomic Sci (2011)

Example pathway illustrating how MetaCyc curators sometimes split pathways into smaller evolutionarily conserved units.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368424&req=5

f1: Example pathway illustrating how MetaCyc curators sometimes split pathways into smaller evolutionarily conserved units.
Mentions: The MetaCyc metabolic database is the reference pathway database used by PathoLogic for pathway prediction [Figure 1]. Version 14.6 (released in November 2010) of MetaCyc contains 1,583 base metabolic pathways and 263 superpathways.

Bottom Line: Both phases draw on the MetaCyc database of metabolic reactions and pathways.MetaCyc contains two data fields to support pathway inference: the expected taxonomic range of each pathway, and a list of key reactions for pathways.These fields have significantly increased the predictive accuracy of PathoLogic.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Group, SRI International 333 Ravenswood Ave, EK207, Menlo Park, CA 94025.

ABSTRACT
The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. The algorithm consists of two phases. The reactome inference phase infers the reactions catalyzed by the organism from the set of enzymes present in the annotated genome. The pathway inference phase infers the metabolic pathways present in the organism from the reactions catalyzed by the organism. Both phases draw on the MetaCyc database of metabolic reactions and pathways. MetaCyc contains two data fields to support pathway inference: the expected taxonomic range of each pathway, and a list of key reactions for pathways. These fields have significantly increased the predictive accuracy of PathoLogic.

No MeSH data available.