Graphics Panel

The Graphics Panel consists of two graphical images: Upper Graph and Lower Graph


Upper Graph

typeWith the Type drop-down menu the user can choose the way of a palindrome/repeat visualization. Three visualization types are available: histograms, noise and pics.

ElementsThe Elements drop-down menu allows the user to choose the type of the structures: palindromes, direct repeats or both.

Gene_chooseThe Gene pane allows the user to browse by the gene PID (Protein Identification Number) or by the gene location.

dna_regionAt the DNA Region pane the user can set up the  DNA region boundaries in nucleotide positions.

At the appeared graph, the line symbolizes DNA sequence. Red color corresponds to genes and white color corresponds to intergenic areas. Upon moving the cursor over genes in the Upper Graph, a pop-up window will present data on the genes based on the .ptt file.



1. With the type Histogram the program depicts histograms of palindrome/repeat density within the specified part of the sequence:


       scaleThe pane Scale shows the number of symbols (in bp) for one histogram bar.


2. With the type Noise the program depicts palindrome/repeat frequencies within the specified part of the sequence:




3. With the type Pics the program depicts every palindrome/repeat by a stand-alone icon. The exact palindromes (stems only) are depicted as blue bars, stem-and-loop structures are depicted as yellow pins, direct repeats are depicted as violet rectangles with width proportional to the repeat length.


Panes Stems, Loops and Repeats shows the number of repeats and palindromes of each type.



Lower Graph

To obtain detailed information about the detected structures the user can select a region (left button down and drag) from the Upper Graph, which will then be depicted in the Lower Graph in an enlarged scale.



Upon moving the cursor over palindromes or direct repeats in the Lower Graph a pop-up window will appear showing structure info in the following order: the sequence, start and end positions, number of times this sequence is found in the whole genome, gene PID if the sequence is found inside a gene or zero if the sequence belongs to an intergenic area.

\Plindrome Info