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)

Select one or more sequence(s) or/and one or more sequence list(s). Note! You cannot create statistics for DNA and protein sequences at the same time, they must be run separately.

Next (figure 18.16), the dialog offers to adjust the following parameters:

Image statisticsstep2
Figure 18.16: Setting parameters for the Sequence statistics tool.

For protein seqences, you can 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.)

You can also choose between two different sets of values for calculation of extinction coefficients:

Read more about calculation of extinction coefficients in section Protein statistics.

Click Finish to start the tool. An example of protein sequence statisticsis shown in figure 18.17.

Image statisticsoutput
Figure 18.17: 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 protein sequence statistics includes:

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. This represents statistics for all codons; however, only codons that contribute with amino acids to the translated sequence will be counted.

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