University of Bielefeld - Technische Fakultät - AG Praktische Informatik

3D Alignment Visualization

Many applications in molecular biology require the detection of a similarity pattern displayed by a number of DNA sequences.
To achieve this aim, scientist perform a so-called multiple alignment. By introducing gaps into the sequences, the alignment software tries to line out similar sections by vertically aligning matching residues in the same column.

An alignment of two sequences can be thought as a unique path through a two dimensional coordinate system, where a residue match results in traversing diagonally, the introduction of a gap in leaving the diagonal (see Figure 1, left).

Figure1: Sequence Alignment Paths

In the case of three sequences, the alignment path can be visualized within a three dimensional cube (see Figure 1, right).

The Java tool Visu3d introduced here, visualizes a three dimensional alignment of short DNA sequences. The cube can be rotated in all three dimensions by using the mouse to point into the desired direction. This applet was used during the Summer 1996 GNA-VSNS Biocomputing course, which pioneered the instruction of students via the Internet.

Please enter three short sequences below and press the button.

Input Java Applet.

View the 3D visualization of the above alignment here.

VisuApp Java Applet. (Use Netscape > 2.0)