Searching and visualising repeats program Oligorep
 The program "Repus" is destined to visualise the results of repeats search  by ReSearch program, and is included in OligoRep program. 

 
 
This program is destined to:
 
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.
Limitations: 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.