• Sequence Comparison and Alignment
  • With DNAMAN, you can compare two or more DNA or protein sequences. Dot matrix comparison provides a graphic view of the similarity of two sequences. Sequence alignment allows you to find homology regions in two or more sequences. You may analyze the homology relationship among the family members using multiple sequence alignment and phylogenetic tree analysis.

  • Dot matrix comparison
  • The Dot Matrix Comparison function compares two DNA sequences or two protein sequences in a dot matrix plot. The abscissa represents one sequence and the ordinate represents the other sequence.

    1. Parameters of dot matrix comparison
    2. Choosing the Sequence | Dot Matrix Comparison command opens a dialog box to input options about the comparison. You may press the Cancel button to show a Sequence Comparison window. In the comparison window, you may modify options by pressing the Option button.

      You may change the following parameters in the Dot Matrix dialog box:

      Click the OK button to validate the parameters and performing comparison.

    3. Comparison methods
    4. DNAMAN may use a quick comparison algorithm to accurately compare two sequences. The parameters are Window size and Mismatch. In order to apply the quick algorithm, the Mismatch must be 0. During comparison, DNAMAN draws a dot where the two sequences are identical with a length equal or more than the Window size. The dot may be shown as a line if identical region is much larger than the Window size. A long line in the matrix indicates a long identical region.

      If the Mismatch is not 0, DNAMAN compares the two sequences progressively from the beginning to end. This is a slower method. During comparison, DNAMAN draws a dot where the two sequences are matched with a length equal or more than the Window size and the mismatch size less than the defined number. The allowed mismatch size is proportional to the length of match size. The dot may be shown as a line if homologue region is much larger than the Window size. A long line in the matrix indicates a long homologue region.

      The default Window size is 10 and Mismatch is 0. Mismatch must be less than half of Window size.



    5. More about dot matrix
    6. You may use different strands for DNA sequence comparison. Two check boxes appear on the window: Seq2+Strand and Seq2-Strand. If nothing is specified, DNAMAN compares the sequence 1 with the + strand of sequence 2. If Seq2-Strand is checked, DNAMAN compares the sequence 1 with the - strand of sequence 2. If both options are checked, DNAMAN compares sequence 1 to both strands of sequence 2. In this case, black dots show the matches between sequence 1 and the + strand of sequence 2, and red dots show matches between the sequence 1 and the - strand of sequence 2.

      You can change the size and shape of the plot. Place the cursor on the low-right corner of the plot. When the cursor switches to , press the left mouse button and drag it to change the size and shape of the plot.

      You can also move the plot within the graphic window. Place the cursor on the up-left corner of the plot. When the cursor switches to , press the left mouse button and drag the plot.

      When the cursor is a cross on the dot matrix plot, the coordinates of Sequence 1 and Sequence 2 are displayed on the left corner of the screen.

      DNAMAN may display the sequences of a selected region on screen. The sequences can be automatically aligned if the homology between the two sequences is high enough. This homology level is set in the Show Sequences section. The default level is 50%. If the Align identity > option is not checked, the two sequences will not be aligned upon selection.