anvi-import-protein-profile

This program imports protein abundance data into a profile database..

🔙 To the main page of anvi’o programs and artifacts.

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 protein abundance profile, such as from proteomic experiments, into a profile-db.

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

• “source” is the source of the protein accessions. It must be a gene function annotation source stored in the anvi’o profile-db (available sources can be found with the program, anvi-db-info).
• “accession” is the protein ID in the annotation source. A contigs database built from a GenBank file, for example, could contain the source, “NCBI_PGAP”, and the accession, “WP_011862028.1”.
• “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 protein abundance value, however defined.

Once protein abundances are stored in a profile database, they can be loaded into a metabolic reaction-network for analysis in the context of biochemical pathways.

Edit this file to update this information.

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.