1. 4.7.1  about analyse (general comments)
  2. 4.7.2  protein properties
  3. 4.7.3  base composition
  4. 4.7.4  codon usage

4.7.1 about analyse

A few utilities for sequence analysis are collected under this menu.

Note that the content of the Analyse menu is dependent upon project type (nucleotide or protein) and on the sequence type currently displayed.

4.7.2 protein properties

This utility analyses the currently displayed protein sequence in a protein project or a translated nucleotide sequence displayed in the main SEQtools editor window. A number of protein properties are included in the form.

The Hydrophopacity menu item includes three different algorithms for calculating the hydropathy plot. The dropdown list allows you to select the width of the sliding window for smoothing of the plot.

4.7.3 base composition

When opened this small form lists the base composition of the currently displad nucleotide sequence. The option is disabled in protein projects.

4.7.4 codon usage

An eleborate function for analysing and using codon usage tables in SEQtools nucleotide and protein projects. In the latter case the menu item is disabled, but the form is opened when back-translating protein sequences into degenerate primers.

In addition to displaying the codon usage table for the displayed protein the function also allows you to build a codon usage table for a particular organism.

The facility is described in the following screenshots.

An open reading frame is identified (see the Translate menu) and highlighted in the sequence displayed below. The second step is to launch the codon usage form.

When the codon usage form opens the highlighted sequence is automatically processed and displayed.

Under the Codon Usage Current tab the codon usage for the selected protein sequence displayed. The popup menu is opened by right-clicking the data field and enables you to display the data in a number of formats.

Note that the currently selected Main codon usage table for the project is "MUS_MUSCULUS.COD" (displayed in the blue title bar of the form). If you wish to add the information for the current protein simply click Build to add (or subtract) the information to the project default table..

If you want to create a new empty table click File/New Codon Usage Table, click File/Open Codon Usage Table to open an existing codon usage table (at the same time making it the default for the project) or add to the currently selected (default) table.

SEQtools uses its own format (*.cut) which in addition to codan usage data also keeps track of the sequences which provided the information; click Info/Codon Table Header to display this information.

The File menu includes options for Printing, Saving and Exporting codon usage files.

As an aid in designing sequencing/PCR primers, it is finally possible to display only the preferred/avoided codons for the table displayed under the Main tab (i.e., for the entire codon usage table). The data are from the Mus musculus codon usage table.

Avoided codons in the Main codon usage table. The data are from the Mus musculus codon usage table.

   2002-2010S.W. Rasmussen  (revised: )