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Secondary Structure Prediction of Proteins |
Palaios, G.A. and Hamodrakas, S.J. |
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Index | |
3. Input Description | |
5. Bug reports and user feedback |
An example of the Text output is shown:
SecStr - Secondary Structure Prediction for TRYPSIN INHIBITOR
|TURN |BETA |HELIX
| DLFBGN | DLFBGN | DLFBGN
| | |
1 R-|*** T T T | . | .
2 P-|*** T T T | . | .
3 D-|*** T T T |* . B | .
4 F-|*** T T T |**. BB |* . H
5 C-|* . T |**. BB |* . H
6 L-|* . T |**. BB |* . H
7 E-|*** T TT |* . B |* . H
8 P-|*** T TT | . | .
9 P-|**** T TTT | . | .
10 Y-|**** T TTT |* . B | .
11 T-|**** T TTT |* . B | .
12 G-|***** T TTTT |**. BB | .
13 P-|**** T T TT |**. BB | .
14 C-|*** T T T |*** BBB |* . H
15 K-|**. T T |**** BBBB |* . H
16 A-| . |***** BBBBB |* . H
17 R-| . |***** BBBBB |* . H
18 I-| . |****** BBBBBB |* . H
19 I-| . |****** BBBBBB |* . H
20 R-| . |***** BBBBB |* . H
21 Y-| . |***** BBBBB |* . H
22 F-|* . T |***** BBBBB |* . H
23 Y-|**. TT |*** BBB | .
24 N-|**. TT |**. BB | .
25 A-|**. TT | . | .
26 K-|* . T |* . B | .
27 A-|* . T |* . B | .
28 G-|* . T |**. B B | .
29 L-| . |**** B BBB | .
30 C-| . |***** B BBBB | .
31 Q-| . |****** BBBBBB |* . H
32 T-| . |****** BBBBBB |* . H
33 F-| . |****** BBBBBB |* . H
34 V-| . |****** BBBBBB |* . H
35 Y-|***** T TTTT |**** BBB B | .
36 G-|***** T TTTT |* . B | .
37 G-|***** T TTTT |* . B | .
38 C-|***** T TTTT | . | .
39 R-|**. TT | . | .
40 A-|* . T | . | .
41 K-|**. T T | . | .
42 R-|**. T T |* . B | .
43 N-|*** TTT |* . B | .
44 N-|*** TTT |* . B | .
45 F-|**. TT |* . B |**. H H
46 K-|**. TT | . |*** H H H
47 S-|*** TTT | . |*** H H H
48 A-|**. T T | . |**** H H HH
49 E-|**. T T |* . B |***** HHH HH
50 D-|**. T T |**. B B |***** HHH HH
51 C-| . |*** BBB |**** HH HH
52 M-| . |*** BBB |**** HH HH
53 R-|**. T T |*** BBB |**. HH
54 T-|**. T T |**. BB |* . H
55 C-|**** T T TT |* . B |* . H
56 G-|**** T T TT | . |* . H
57 G-|**** T T TT | . | .
58 A-|**** T T TT | . | .
The text output contains:
(a) Individual methods' predictions for each secondary
structure type (beta-turn [T], beta-strand [B] and alpha-helix [H]).
(b) Histograms (shown as asterisks)
of the number of methods assigning each residue to a given
secondary structure type.
The Joint Prediction Histogram of the results of the six Secondary Structure Prediction Methods is represented by the SecStrChart Java Applet. The most probable structures , predicted by three or more methods, are painted blue in the joint prediction histograms.