Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.

ABSTRACT: The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, we have reconstructed a genome-scale model of its metabolism. This model consists of 836 metabolic genes, 257 pathways, 6 cellular compartments, and is supported by extensive manual curation of 491 literature citations. To aid our reconstruction, we developed three optimization-based algorithms, which together comprise Fast Automated Reconstruction of Metabolism (FARM). These algorithms are: LInear MEtabolite Dilution Flux Balance Analysis (limed-FBA), which predicts flux while linearly accounting for metabolite dilution; One-step functional Pruning (OnePrune), which remo

SUBMITTER: Dreyfuss JM 

PROVIDER: S-EPMC3730674 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature