Team:Virginia/Model/ModelSEED


ModelSEED / What's in a name?

ModelSEED is an online tool for creation, analysis and optimization of high-throughput whole-genome metabolic models. To begin, RAST-annotated genome data are required (see below). These data contain highly accurate information about almost all genes in the genome and their functions in the organism. ModelSEED takes the annotated genome as an input and applies a series of algorithms to reconstruct the genome-scale metabolic model of the organism based on the known biochemical reactions and a user-specified medium. That way, the user has the choice of which nutrients are available for uptake by the cell.

FIG

  • FIG stands for Fellowship for Interpretation of Genomes. It is a non-profit organization whose aim is to provide support to researchers who analyze genomes. More details here
  • FIG maintains a collection FIGfams -- functionally related families of proteins, e.g. in biochemical pathways.

RAST

  • RAST stands for Rapid Annotation using Subsystem Technology
  • A free, first-come first-serve online tool for annotation of bacterial genomes. Data need to be uploaded to RAST before use in ModelSEED
  • Accepts both FASTA (un-annotated DNA sequence) and Genbank (annotated) genome formats. Existing genecalls in Genbank file may be preserved by choosing the appropriate option.