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Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED

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Systems Metabolic Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 985))

Abstract

Over the past decade, genome-scale metabolic models have proven to be a crucial resource for predicting organism phenotypes from genotypes. These models provide a means of rapidly translating detailed knowledge of thousands of enzymatic processes into quantitative predictions of whole-cell behavior. Until recently, the pace of new metabolic model development was eclipsed by the pace at which new genomes were being sequenced. To address this problem, the RAST and the Model SEED framework were developed as a means of automatically producing annotations and draft genome-scale metabolic models. In this chapter, we describe the automated model reconstruction process in detail, starting from a new genome sequence and finishing on a functioning genome-scale metabolic model. We break down the model reconstruction process into eight steps: submitting a genome sequence to RAST, annotating the genome, curating the annotation, submitting the annotation to Model SEED, reconstructing the core model, generating the draft biomass reaction, auto-completing the model, and curating the model. Each of these eight steps is documented in detail.

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Acknowledgements

We acknowledge the entire SEED, Model SEED, and CytoSEED teams at Argonne National Laboratory, Fellowship for Interpretation of Genomes, Hope College, and University of Chicago for efforts on the frameworks described in this chapter. This work was supported by the US Department of Energy under contract DE-ACO2-06CH11357 (SD, CH), the National Institute of Allergy and Infectious Diseases under contract HHSN266200400042C (RO), and the National Science Foundation under grants MCB-0745100 and DBI-0850546 (MD, AB, VV, RO).

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Authors and Affiliations

  1. MCS Division, Argonne National Laboratory, Argonne, IL, USA

    Scott Devoid & Christopher Henry

  2. Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA

    Ross Overbeek & Veronika Vonstein

  3. Department of Computer Science, Hope College, Holland, MI, USA

    Matthew DeJongh

  4. Department of Biology, Hope College, Holland, MI, USA

    Aaron A. Best

Authors
  1. Scott Devoid
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  2. Ross Overbeek
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  3. Matthew DeJongh
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  4. Veronika Vonstein
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  5. Aaron A. Best
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  6. Christopher Henry
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Corresponding author

Correspondence to Christopher Henry .

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Editors and Affiliations

  1. Cockrell School of Engineering, Dept. of Chemical Engineering, The University of Texas at Austin, E. Dean Keeton Street 200, Austin, 78712, Texas, USA

    Hal S. Alper

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Devoid, S., Overbeek, R., DeJongh, M., Vonstein, V., Best, A.A., Henry, C. (2013). Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED. In: Alper, H. (eds) Systems Metabolic Engineering. Methods in Molecular Biology, vol 985. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-299-5_2

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  • DOI: https://doi.org/10.1007/978-1-62703-299-5_2

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-298-8

  • Online ISBN: 978-1-62703-299-5

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