- This program is destined
|1) search the direct, inverse,
complementary and symmetric substring copies (repeats) in a target DNA sequence;
2) visulaize the results obtained in 1) with the help of
Java-designed viewer applet. The repeats searched are subject to the statistical
significance based on the binomial distibution (Soloviev V.V., Zharkikh A.A.,
Kolchanov N.A., Molek.Biol.(Russ), 1985, v.19, N.2, p.524-528). The repeats with the
length exceeding the significance threshold (0.05) are considered only.
The sequence length should not exceed 32kB.
- Visualizing information
|The target sequence is
represented by the scale line containing the nucleotide positions. The repeats found are
represented by arrow lines, pointing to the 5'-3' destiny. For each repeat the separate
string is reserved consisting of two lines corresponding to the direct and complementary
strands of the target DNA sequence. Four types of repeats are taken into account: direct,
complementary, symmetrical, inverse, (Each type has definite color). Double clicking on
the repeat image location a window is created containing the repeat features, namely: a)
the nucleotide substring of the repeat copies, matched nucleotides high - colored. b) The
start - end positions of repeat copies, their orientation and number of the length (L) and
matched (K) positions. The window could be dragged with the mouse in the proper place on
the screen. Should one to observe a range of repeats there is a possibility to create
additional information windows (see Menu Items). For scanning the next part of sequence
(not rested in current window) the mouse dragging should be performed in the desirable
destination of scanning. To accommodate the quick repeat location the projection line is
created by clicking at the scale line within repeat location.
Menu The initiation of menu is performed by clicking
on the rectangle in the low right corner of the window. The menu items include
- 1) Items for rescaling the drawing image;
- 2) Item for adding the new information window.