FT - Study of Residue Periodicities in Sequences 		Pasquier, C.M., Promponas, V.I.,
Varvayannis, N.J. and Hamodrakas, S.J.
Index 3. Description of the Input 5. Examples of use

4. Description of the Output

The output page summarizes the input data used by the program and displays the result of the calculation.

4.1 Summary of the query data

After the title of the sequence (if one is specified in the input form), a view of the selected residues in the sequence is displayed. If 1-letter code is used, the sequence is printed with fourty residues per line. Each selected residue is represented by its 1-letter code and non selected residues are represented by a dot. For example, if residues 'A' and 'L' are selected in the sequence:

  MSTESMIRDV ELAEEALPKK TGGPQGSRRC LFLSLFSFLI VAGATTLFCL LHFGVIGPQR
  EEFPRDLSLI SPLAQAVRSS SRTPSDKPVA HVVANPQAEG QLQWLNRRAN ALLANGVELR
  DNQLVVPSEG LYLIYSQVLF KGQGCPSTHV LLTHTISRIA VSYQTKVNLL SAIKSPCQRE
  TPEGAEAKPW YEPIYLGGVF QLEKGDRLSA EINRPDYLDF AESGQVYFGI IAL

then the representation of the selected residues is displayed like this:

               1         2         3         4
      1234567890123456789012345678901234567890
  000 ...........LA..AL.............L.L.L...L.
  001 .A.A..L..LL...............L.L...LA.A....
  002 .........A...A...A...L..L...A.ALLA....L.
  003 ...L......L.L.....L...........LL.......A
  004 ........LL.A............A.A........L....
  005 .L.....L.A.......L..A..........AL

If the 3-letter code is used, only ten residues per line are displayed. Each selected residue is represented by its 3-letter code and non selected residues are represented by three dots. The example above is displayed in the following way:

       1   2   3   4   5   6   7   8   9   0
  000 ... ... ... ... ... ... ... ... ... ... 
  001 ... LEU ALA ... ... ALA LEU ... ... ... 
  002 ... ... ... ... ... ... ... ... ... ... 
  003 LEU ... LEU ... LEU ... ... ... LEU ... 
  004 ... ALA ... ALA ... ... LEU ... ... LEU 
  005 LEU ... ... ... ... ... ... ... ... ... 
  006 ... ... ... ... ... ... LEU ... LEU ... 
  007 ... ... LEU ALA ... ALA ... ... ... ... 
  008 ... ... ... ... ... ... ... ... ... ALA 
  009 ... ... ... ALA ... ... ... ALA ... ... 
  010 ... LEU ... ... LEU ... ... ... ALA ... 
  011 ALA LEU LEU ALA ... ... ... ... LEU ... 
  012 ... ... ... LEU ... ... ... ... ... ... 
  013 LEU ... LEU ... ... ... ... ... LEU ... 
  014 ... ... ... ... ... ... ... ... ... ... 
  015 LEU LEU ... ... ... ... ... ... ... ALA 
  016 ... ... ... ... ... ... ... ... LEU LEU 
  017 ... ALA ... ... ... ... ... ... ... ... 
  018 ... ... ... ... ALA ... ALA ... ... ... 
  019 ... ... ... ... ... LEU ... ... ... ... 
  020 ... LEU ... ... ... ... ... LEU ... ALA 
  021 ... ... ... ... ... ... ... LEU ... ... 
  022 ALA ... ... ... ... ... ... ... ... ... 
  023 ... ALA LEU

The other input data are displayed in the lines below:

4.2 Display of the results in a table

The result of the computation is displayed in a eight columns table.

n
The order of the Fourier transform. This variable is equal to the embedding size divided by the period.
a
Real part of the complex number representing the wave.
b
Imaginary part of the complex number representing the wave.
r
The norm of the complex number. It is equal to SQR(a^2 + b^2).
theta
This is the angle formed by the vector that represents this complex number in an x-y surface. The tangent of theta should be equal to b/a.
origin
(see McLachlan, 1977)
period
period shows the periodicity of a selected residue or group of residues in the selected part of the sequence.
intensity
intensity is equal to a^2 + b^2. The probability of a random calculation of a periodicity is equal to exp(-I), where I is the intensity calculated for this periodicity.

4.3 Display of the results with a graph

The graphical representation of the result shows on a graph the periodicities on the X-axis and the Intensities on the Y-axis. If the cutoff (or minimum intensity) is equal to zero, a continuous graph is displayed, otherwise a bar graph is used.