anvi-import-metabolite-profile

This program imports metabolite abundance data and stores it in a profile database..

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Authors

Can consume

profile-db

Can provide

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program imports a metabolite abundance profile, such as from metabolomic experiments, into a profile-db.

This program takes as input a tab-delimited file of metabolite abundance data and a profile-db. The tabular file must have three columns with the following names: “accession”, “sample”, and “abundance”. Each row of the table corresponds to a distinct metabolite abundance measurement.

• “accession” is the ModelSEED Compound ID, e.g., “cpd00027” for D-glucose.
• “sample” is the name of the sample in which the measurement was made. It need not be the same as any nucleotide sequence samples stored in the profile database.
• “abundance” is the metabolite abundance value, however defined.

Once metabolite abundances are stored in a profile database, they can be loaded into a metabolic reaction-network for analysis in the context of biochemical pathways. Metabolites in the network are defined in terms of ModelSEED Compounds.

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Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.