title: Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.
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.
authors: MCS Division, Argonne National Laboratory, Argonne, IL, USA.
authors: Scott
authors: S
authors: Devoid
authors: Ross
authors: R
authors: Overbeek
authors: Matthew
authors: M
authors: DeJongh
authors: Veronika
authors: V
authors: Vonstein
authors: Aaron A
authors: AA
authors: Best
authors: Christopher
authors: C
authors: Henry
mesh_terms: D030541:Databases, Genetic; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods*; D009862:Online Systems; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface