Actually a protein report is a collection of some of the protein analyses which are described elsewhere in this help function.
To create a protein report do the following:
Toolbox | Classical Sequence Analysis () | Protein Analysis ()| Create Protein Report ()
This opens dialog Step 1, 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 dialog Step 2 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.
- Sequence statistics. See Protein statistics for more about this topic.
- Plot of charge as function of pH. See Protein charge for more about this topic.
- Plot of hydrophobicity. See Hydrophobicity for more about this topic.
- Plot of local complexity. See Local complexity plot for more about this topic.
- Dot plot against self. See Dot plots for more about this topic.
- Secondary structure prediction. See Secondary structure prediction for more about this topic.
- Pfam domain search. See Pfam domain search for more about this topic.
- Local BLAST. See Local BLAST for more about this topic.
- NCBI BLAST. See NCBI BLAST for more about this topic.
When you have selected the relevant analyses, click Next. Step 3 to Step 7 (if you select all the analyses in Step 2) are adjustments of parameters for the different analyses. The parameters are mentioned briefly in relation to the following steps, and you can turn to the relevant chapters or sections (mentioned above) to learn more about the significance of the parameters.
In Step 3 you can adjust parameters for sequence statistics:
- Individual Statistics Layout. Comparative is disabled because reports are generated for one protein at a time.
- Include Background Distribution of Amino Acids. Includes distributions from different organisms. Background distributions are calculated from UniProt www.uniprot.org version 6.0, dated September 13 2005.
In Step 4 you can adjust parameters for hydrophobicity plots:
- Window size. Width of window on sequence (odd number).
- Hydrophobicity scales. Lets you choose between different scales.
In Step 5 you can adjust a parameter for complexity plots:
- Window size. Width of window on sequence (must be odd).
In Step 6 you can adjust parameters for dot plots:
- Score model. Different scoring matrices.
- Window size. Width of window on sequence.
In Step 7 you can adjust parameters for Pfam domain search:
- Database and search type. Lets you choose different databases and specify the search for full domains or fragments. See Pfam search parameters for more info about this topic.
- Significance cutoff. Lets you set your E-value. See Pfam search parameters for more info about this topic.
In Step 8 you can adjust parameters for BLAST search:
- Program. Lets you choose between different BLAST programs.
- Database. Lets you limit your search to a particular database.