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Annotate Domains in a Genome


Annotate a Genome object with protein domains from widely used domain libraries.

This App identifies protein domains from widely used domain libraries. It requires a Genome as input, which must already have annotated protein-encoding genes (e.g., those identified using the Annotate Microbial Genome or Annotate Microbial Assembly Apps).

The user must choose one of the following sets of models with which to annotate their Genome:

For the first four libraries above (COGs, CDD, SMART and PRK), KBase runs RPS-BLAST version 2.2.31, from the BLAST+ package at NCBI, identifying all domain hits with an E-value of 10-4 or better.

For the three HMM libraries (Pfam, TIGRFAMs and NCBIfam), KBase runs HMMER version 3.1b2, identifying all domain hits at least as significant as the family-specific trusted cutoff identified by the curators of each model.

The annotation job may run for a few hours depending on the total number of libraries selected and/or the size of the genome. When the annotation job finishes, a DomainAnnotation object will be stored in your data panel, which can be used to browse the domains that were identified in your genome.

Annotate Domains in a Genome Output
The output report currently consists of two tabs:

The user can download the annotations in CSV (comma separated values) format. The fields in this CSV file are as follows:

Team members who developed & deployed this App in KBase: John-Marc Chandonia, Roman Sutormin, and Pavel Novichkov. For questions, please contact us.

Related Publications

App Specification:

Module Commit: 46df12c6f8b16ae25df386c05e78c94292121db2