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. 2011 Dec 31;5(3):424-9.
doi: 10.4056/sigs.1794338. Epub 2011 Dec 23.

The pathway tools pathway prediction algorithm

Peter D Karp  1 , Mario Latendresse, Ron Caspi
Affiliations

The pathway tools pathway prediction algorithm

Peter D Karp et al. Stand Genomic Sci. .

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.

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Figures

Figure 1
Figure 1
Example pathway illustrating how MetaCyc curators sometimes split pathways into smaller evolutionarily conserved units.
See this image and copyright information in PMC

References

    1. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee T, Kaipa P, Gilham F, Spaulding A, Popescu L, et al. Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief Bioinform 2010; 11:40-79; .10.1093/bib/bbp043 - DOI - PMC - PubMed
    1. Dale JM, Popescu L, Karp PD. Machine learning methods for metabolic pathway prediction. BMC Bioinformatics 2010; 11:15 10.1186/1471-2105-11-15 - DOI - PMC - PubMed
    1. BioCyc Database Collection http://BioCyc.org/
    1. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2010; 38:D473-D479 10.1093/nar/gkp875 - DOI - PMC - PubMed
    1. MicroCyc home page. https://www.genoscope.cns.fr/agc/microscope/metabolism/microcyc.php

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