• Codon usage analysis
  • You may analyze the codon usage of a DNA sequence in a specific reading frame. You may also save and open a codon usage table.

    1) Display codon usage

    Choose the Protein | Codon Usage | Reading Frame 1 or Reading Frame 2 or Reading Frame 3 command to display the codon usage table of the current sequence. The codon usage table is shown in a graphic window.

    As reference of the table, DNAMAN shows the sequence name, translation region and the reading frame number. The total codon number is also indicated. In the table, the first codons are listed at left, the second on top and the third at right. The codon usage is shown as Amino acid Number/ Frequency(in 1000)/ Preference(in 100).

    Amino acid: the amino acid translated from the codon

    Number: the codon number presented in the sequence

    Frequency(in 1000): the codon frequency in the sequence

    Preference(in 100): the codon percentage preference for the amino acid

    Example: the GUG codon in a sequence of 357 amino acids shows as V 10/28/53.

    Interpretation:

    V: GUG codes for Valine (V)

    10: there are 10 GUG codons in the sequence

    28: GUG represents 2.8% in the sequence (10/357) .

    53: GUG represents 53% of codons coding for Valine (V).

    DNAMAN analyze only the Analysis Region of the current sequence. If an open reading frame is known, you may use the Sequence | Current Channel | Analysis Definition command to define the open reading frame of the current DNA sequence.

    The codon usage table is drawn in a graphic window, you may modify the graphic content. See the section V.1 for adding text objects to the codon usage table.

    2) Save/Append Codon usage file

    You may save a codon usage table to a file or add the current codon usage to an existing table. Choose the Protein | Save/Append Codon Usage File command to open a File Open dialog box. You may enter a new file name to save the codon usage table to a file, or select an existing file to append the codon usage to the table.

    The codon usage file can be used for reverse translation (See the section XI.4 -Reverse Translation).

    3) Open Codon usage file

    Choose the Protein | Open Codon Usage File command to open a File Open dialog box. Select an existing codon usage file and click the Open button. DNAMAN shows the codon usage table in a graphic window, as described in the Display Codon Usage section.