Model SEED protocols

Model SEED specifications


Unique identifier OMICS_05183
Name Model SEED
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Henry CS <>

Publication for Model SEED

Model SEED IN pipelines

PMCID: 5433236
PMID: 28506279
DOI: 10.1186/s40168-017-0271-9

[…] eew40126, ehl93080, egq26304) were aligned in clustal omega [17] and used to construct hidden markov models (hmm) on full-length proteins via hmmbuild (default mode, hmmer 3.1b1, model seed sequences were realigned to the model using hmmalign (default mode) and manually checked in jalview (, v. 2.8.1) before rebuilding models based on the obtained alignments; […]

PMCID: 3444828
PMID: 22997515
DOI: 10.1155/2012/323472

[…] a minimal set of reactions to add from a universal database so that a specified set of metabolites may be produced. these optimization-based procedures have already been integrated into the model seed metabolic reconstruction pipeline with some success [7]. reed et al. [8] utilize a method that adds a minimum-sized set of reactions from a universal database that allows for a specified […]

Model SEED institution(s)
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA

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