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Domain Annotation Object Info
kb_ObjectInfo

v.1.2.1

By: landml

Launch

Create text info files based on a DomainAnnotation object.

The intended purpose of this App is to produce a downloadable TEXT file about a Domain Annotation object.

Most KBase data objects already have some type of viewable HTML table, either as output from an App or by dragging the object onto the Narrative. This App serves a different purpose. This App creates data files that are downloadable and used with local tools such as Excel or informatic scripts.

This App creates files on the annotated domains associated with a Genome. A Summary section has a preview of the full output. It is intended to be a preview of the downloadable file. If the file is tab or comma delimited, it may appear misaligned on the screen but readable by a computer script. The HTML link opens a new tab with the full output. The link for downloading the files is in the Files section of the output.

The inputs are:

The outputs are:

  1. The frequency count of each Domain in the annotation file.
  2. Two downloadable files in the Files section:
    1. A list of the frequency counts (same as the Summary above)
    2. A list of the genes and their predicted domains. One line per gene and domain combination. The list of columns includes the identities of the contig, gene, and domain, the location of the gene, the E-value of the domain hit, the domain name, and higher levels of aggregation for the domain. For example, COG0021, has a domain name of 'Transketolase' and is categorized in the G category (Carbohydrate transport and metabolism), and is part of the general category of METABOLISM.

NOTE: This file will include all domains that were in the Domain Annotation App output. The App may have included just one domain model source (e.g. TIGRFAM) or it may have included all available sources. If only one source was included in the annotation App, this file will only include that one source.

Related Publications


App Specification:

https://github.com/kbaseapps/kb_ObjectInfo/tree/e9d2566b748fd735590f131da284ca44aaf5aefb/ui/narrative/methods/domain_report

Module Commit: e9d2566b748fd735590f131da284ca44aaf5aefb