Sequence statistics

CLC Genomics Workbench can produce an output with many relevant statistics for protein sequences. Some of the statistics are also relevant to produce for DNA sequences. Therefore, this section deals with both types of statistics. The required steps for producing the statistics are the same.

To create a statistic for the sequence, do the following:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | General Sequence Analysis (Image generalsequenceanalyses)| Create Sequence Statistics (Image proteinreport)

This opens a dialog where you can alter your choice of sequences. If you had already selected sequences in the Navigation Area, these will be shown in the Selected Elements window. However you can remove these, or add others, by using the arrows to move sequences in or out of the Selected Elements window. You can also add sequence lists.

Note! You cannot create statistics for DNA and protein sequences at the same time; they must be run separately.

When the sequences are selected, click Next.

This opens the dialog displayed in figure 14.19.

Image statisticsstep2
Figure 14.19: Setting parameters for the sequence statistics.

The dialog offers to adjust the following parameters:

You can also choose to include Background distribution of amino acids. If this box is ticked, an extra column with amino acid distribution of the chosen species, is included in the table output. (The distributions are calculated from UniProt version 6.0, dated September 13 2005.)

Click Next if you wish to adjust how to handle the results. If not, click Finish. An example of protein sequence statisticsis shown in figure 14.20.

Image statisticsoutput
Figure 14.20: Example of protein sequence statistics.

Nucleotide sequence statistics are generated using the same dialog as used for protein sequence statistics. However, the output of Nucleotide sequence statistics is less extensive than that of the protein sequence statistics.

Note! The headings of the tables change depending on whether you calculate 'individual' or 'comparative' sequence statistics.

The output of comparative protein sequence statistics include:

The output of nucleotide sequence statistics include:

If nucleotide sequences are used as input, and these are annotated with CDS, a section on Codon statistics for Coding Regions is included.

A short description of the different areas of the statistical output is given in Bioinformatics explained: Protein statistics.