merlin

merlin reconstructs genome-scale metabolic models (GEMs) from annotated genomic sequences to enable metabolic network reconstruction and analysis.

Key Features:

• Functional Genomic Annotation: Performs comprehensive functional genomic annotation, including identification of genes encoding transport proteins and generation of corresponding transport reactions.
• Compartmentalization: Predicts protein subcellular localization to assign metabolites and reactions to appropriate cellular compartments based on enzyme localization.
• Gene-Protein-Reaction (GPR) Associations: Automatically generates gene–protein–reaction (GPR) associations and integrates them into the model.
• Model Export: Exports draft metabolic models in the SBML standard format.
• Template-Based and De Novo Reconstructions: Supports both template-based and de novo draft reconstructions for organisms with varying levels of characterization.
• Integration of Algorithms and Third-Party Tools: Incorporates advanced algorithms and third-party tools for genome functional annotation, draft assembly, and model refinement applicable to eukaryotic and prokaryotic species.

Scientific Applications:

• Genome-Scale Model Reconstruction: Enables reconstruction of genome-scale metabolic models for prokaryotes and eukaryotes.
• Genome Metabolic Annotation and Re-annotation: Supports generation and refinement of genome metabolic annotations from sequence data.
• Transport and Compartmentalized Metabolism Studies: Facilitates modeling of transport processes and compartmentalized metabolic networks via transport reaction generation and subcellular localization prediction.
• Biotechnology and Biomedical Research: Supports investigations of metabolic network implications in health, disease, and biotechnology applications.

Methodology:

Computational steps explicitly include functional genomic annotation; identification of transport-encoding genes and generation of transport reactions; prediction of protein subcellular localization; automatic generation of GPR associations; template-based and de novo draft reconstruction; export to SBML; and integration of third-party algorithms for genome annotation, draft assembly, and model refinement.