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SSPRED: program of secondary structure prediction

Neural nets based on profile of psiBLAST comparison of the query sequence with NR database.

Output example:

>T0388
Length=174
                                                               
 PredSS                   bbbbb       aa     bbbbbbbb      aaa
 AA seq     ENLYFQSMINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRN
 ProbA      00242002220000000000000000552110000000000110000766
 ProbB      00002200000334888851103452000100499999985010000000
                                                               
 PredSS     aaaaaaaaaaaa   bbbbbbb           aaaaaaaaaa    bbb
 AA seq     YLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFP
 ProbA      77999999998520000000000121301000089899999971100000
 ProbB      00000000000000389999873100000000000000000000104879
                                                               
 PredSS     bb           aaaaaaaa          bbbbb    bbbbbb    
 AA seq     IFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEE
 ProbA      00100000010115888787643000000000000000000000000000
 ProbB      86453442200000000000000000133438988920008999983000
                                     
 PredSS      aaaaaaaaaaaaaaaaaa     
 AA seq     PIEVIRPDIAALVRQVIIKKKEDL
 ProbA      055688999999999997743000
 ProbB      000000000000000000000000
 

Where:
PredSS - secondary structure predicted: a - alpha helix, b - beta sheet;
AA seq - amino acid sequence in one-letter form;
ProbA - probability of 'a' structure for the position,
ProbB - probability of 'b' structure for the position.

>T0388
Length=174
   1 E C 0 0
   2 N C 0 0
   3 L C 2 0
   4 Y C 4 0
   5 F C 2 2
   6 Q C 0 2
   7 S C 0 0
   8 M C 2 0
   9 I C 2 0
  10 N C 2 0
  11 S C 0 0
  12 F C 0 3
  13 Y C 0 3
  14 A C 0 4
  15 F B 0 8
  16 E B 0 8
  17 V B 0 8
  18 K B 0 8
  19 D B 0 5
  20 A C 0 1
  21 K C 0 1
  22 G C 0 0
  23 R C 0 3
  24 T C 0 4
  25 V C 0 5
  26 S C 0 2
  27 L A 5 0
  28 E A 5 0
  29 K C 2 0
  30 Y C 1 1
  31 K C 1 0
  32 G C 0 0
  33 K C 0 4
  34 V B 0 9
  35 S B 0 9
  36 L B 0 9
  37 V B 0 9
  38 V B 0 9
  39 N B 0 9
  40 V B 0 8
  41 A B 0 5
  42 S C 1 0
  43 D C 1 1
  44 C C 0 0
  45 Q C 0 0
  46 L C 0 0
  47 T C 0 0
  48 D A 7 0
  49 R A 6 0
  50 N A 6 0
  51 Y A 7 0
  52 L A 7 0
  53 G A 9 0
  54 L A 9 0
  55 K A 9 0
  56 E A 9 0
  57 L A 9 0
  58 H A 9 0
  59 K A 9 0
  60 E A 9 0
  61 F A 8 0
  62 G A 5 0
  63 P C 2 0
  64 S C 0 0
  65 H C 0 3
   
   

Where:
1 column - a number of position,
2 column - amino acid sequence in one-letter form,
3 column - secondary structure predicted: A - alpha helix, B - beta sheet;
4 column - probability of 'A' structure for the position,
5 column - probability of 'B' structure for the position.