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.
Highlights
The MetaCyc Pathway DatabaseThe MetaCyc metabolic database is the reference pathway database used by PathoLogic for pathway prediction [Figure 1]
We describe the metabolic pathway prediction algorithm used by the Pathway Tools software [1,2]
Reactome Inference The first step in pathway prediction is to infer the set of biochemical reactions that can be catalyzed by the enzymes encoded by the genome, that is, to infer the reactome of the organism
Summary
The MetaCyc Pathway DatabaseThe MetaCyc metabolic database is the reference pathway database used by PathoLogic for pathway prediction [Figure 1]. The Genomic Standards Consortium forming a pathway prediction in organism B, and B contained enzymes for reactions R4–R6, we would predict P1 as present in B. Reactome Inference The first step in pathway prediction is to infer the set of biochemical reactions that can be catalyzed by the enzymes encoded by the genome, that is, to infer the reactome of the organism.
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