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G-Squares

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Instructions for use of the “G-Squares” program


The program provides a pictorial view of DNA sequences. Whole genomes, individual chromosomes or shorter DNA sequences can be visualized. It can be used in any computer provided with JAVA.
The output contains four items:
  • A table with the relative frequency of some DNA dimers. Several DNA sequences can be compared.
  • A 4x4 square with the frequency of dimers for each individual sequence (D-square).
  • A 4x4 square with the frequency of R,Y tetramers (R=purine; Y=pyrimidine) for each individual sequence (RY-square).
  • A 16x16 square with the frequency of all tetramers for each individual sequence (T-square).
The program requires as input DNA sequences in any text format, but they should be labelled with the “ .fasta” extension. Files in a different format should be saved as a text file and named with the “ .fasta” extension.
Operation of the program
  1. Open the program in the computer
  2.  Click on “ examinar” and introduce a sequence.
  3. If you want to introduce other sequences, click again on “ examinar” . Up to 20 sequences can be simultaneously examined.
  4. A table with the numerical results appears. It may be printed or stored as a figure in .jpg format.
  5. In order to obtain the graphical squares, you should click on the desired sequence, using the right button of the computer mouse.
  6. In order to store the squares (also in .jpg format), you should click on the option “ guardar” .
 
Explanation of the output
The numerical table gives the ratio of frequencies of dimers in the sequence under
study. The two lower rows give the relative preference for alternation:
Frequency of (YR+RY)
ALT = (YR+RY)/(RR+YY)
In general ALT is <1, since most genomes favour polypurine/polypyrimidine sequences.
The frequency of each sequence is multiplied by 104 in the 4x4 squares. The average value is 104/16 = 625. In the 16x16 squares it is multiplied by 105, so that the average value is 105/256 = 391. The range of colours in the figures is the following:
RY squares: blue >900, 701-900, 551-700, 401-550 and <400 white.
D and T-squares: red>1500, 1001-1500, 701-1000, 601-700, 501-600, 401-500, 301-400,
101-300, <100 white.

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