Build Functional Profile
To compute the number of reads in a sample mapping to regions involved with Pfam domains or GO terms, you can run the "Build Functional Profile" by going to:
Toolbox | Microbial Genomics Module (
) | Whole Metagenome Analysis (beta) (
) | Build Functional Profile (
)
The following parameters can then be set:
- Reference. A reference set of contigs annotated with Pfam domains and/or BLAST hits. If the read mapping contains an annotated genome, this parameter is optional.
- GO database. The GO database, used to map between Pfam domains and GO terms. The GO database can be downloaded using the "Download GO Database" tool (see section "Download GO database" ).
- GO subset. A subset of the GO database. Since many GO terms are too general or too specific, several meaningful subsets of GO terms are provided. See http://geneontology.org/page/go-slim-and-subset-guide.
- Propagate GO mapping. When selected, Pfam annotations are mapped to the relative GO terms and all their more general terms. For example, the Pfam domain "CutC" maps to the GO term "0005507 // copper ion binding". If Propagate GO mapping is enabled, the tool would also map to more general GO terms such as "0055070 // copper ion homeostasis", "0055076 // transition metal ion homeostasis", and "0065007 // biological regulation".
You can then select which output elements should be generated.
- Create Pfam functional profile. The functional profile obtained by counting reads overlapping Pfam domains.
- Create GO functional profile. The functional profile obtained by counting reads overlapping GO terms. Note that a database must be specified in order to build a GO functional profile, as preexisting GO annotations on pfam domains are ignored by the tool.
- Create BLAST hit functional profile. The functional profile obtained by counting reads overlapping BLAST hits.
- Create Report. A report stating statistics about the input reference contigs and read mapping, as well as the number of matches to each feature.
The resulting functional abundance tables store the number of reads corresponding to each Pfam domain, GO term or best BLAST hit. The data can be explored using Stack Visualization and Sunburst plots, similarly to OTU abundance tables (see section "Visualization of the OTU abundance table").