Running Pfam Domain Search

When you have downloaded the Pfam database you are ready to perform a Pfam domain search. To do this start the Pfam search tool:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Protein Analysis (Image proteinanalyses)| Pfam Domain Search (Image pfam)

If a sequence was selected before choosing the Toolbox action, this sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.

You can perform the analysis on several protein sequences at a time. This will add annotations to all the sequences. Click Next to adjust parameters (see figure 16.10).

Image pfam_step2
Figure 16.10: Setting parameters for Pfam Domain Search.

Click Next to adjust the output of the tool. The Pfam search tool can produce two types of output. It can add annotations on the input sequences that show the domains found (see figure 16.11) and it can output a table with all the domains found.

Click Finish to start the tool.

Image pfam_output
Figure 16.11: Annotations (in red) that were added by the Pfam search tool.

Domain annotations added by the Pfam search tool have the type Region. If the annotations are not visible they have to be enabled in the side panel. Detailed information for each domain annotation, such as the bit score which is the basis for the prediction of domains, is available through the annotation tool tip.

A more detailed description of the scores provided in the annotation tool tips can be found here: