Protein report

CLC Genomics Workbench is able to produce protein reports, a collection of some of the protein analyses described elsewhere in this manual.

To create a protein report do the following:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Protein Analysis (Image proteinanalyses)| Create Protein Report (Image proteinreport)

This opens a dialog where you can choose which proteins to create a report for. If you had already selected a sequence in the Navigation Area before running the Toolbox action, this will be shown in the Selected Elements. However, you can use the arrows to change this. When the correct one is chosen, click Next.

In the next dialog, you can choose which analyses you want to include in the report. The following list shows which analyses are available and explains where to find more details.

When you have selected the relevant analyses, click Next. In the following dialogs, adjust the parameters for the different analyses you selected. The parameters are explained in more details in the relevant chapters or sections (mentioned in the list above).

For sequence statistics:

For hydrophobicity plots:

For complexity plots:

For dot plots:

For Pfam domain search:

For BLAST search:

Also set the BLAST parameters as explained in Local BLAST.

For BLAST against NCBI databases:

Also set the BLAST parameters as explained in NCBI BLAST.

An example of Protein report can be seen in figure 16.14.

Image proteinreportoutput
Figure 16.14: A protein report. There is a Table of Contents in the Side Panel that makes it easy to browse the report.

By double clicking a graph in the output, this graph is shown in a different view (CLC Genomics Workbench generates another tab). The report output and the new graph views can be saved by dragging the tab into the Navigation Area.

The content of the tables in the report can be copy/pasted out of the program and e.g. into Microsoft Excel. You can also Export (Image previous_folder_16_n_p) the report in Excel format.