HELP AND SAMPLE OUTPUT
Input Sequence
Paste one letter amino acid sequence in the box provided here.
Method of prediction
You can select any one method for prediction from a list of 5 methods and can also select the option "All" that will predict beta-turns by using all the listed methods simultaneously and will give you a consensus sequence that will be predicted as beta-turn by all the methods.
The prediction results are in the form of HTML pages that will be returned to the user within a few seconds.There are 3 options for output:
A sample output page can be viewed below:
Nomenclature
AA = the amino acid sequence (as submitted by user)
S. No. = serial numbers of the predicted turns
Turn = amino acid sequence of the segment forming the turn
Position = position number of the residues in the turn
Residue numbers are indicated by a scale above the sequence (written as 10,20,30 ...).
Predicted location of ß-turns
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AA HKFLDSFDEPDLFIRDEKFDISTWEIARFCNVMHDSKFLYQWIEDPWQDSWQDEIWDE
S.No Turn Position
1 DSFD 5-8
2 EPDL 9-12
3 HDSK 34-37
4 DSKF 35-38
5 DPWQ 45-48
6 WQDS 47-50
7 QDSW 48-51
8 DSWQ 49-52
Nomenclature
AA = the amino acid sequence (as submitted by user)
F1 = first frame
F2 = second frame
F3 = third frame
F4 = third frame
The graphical (frames) output is displayed in rows. Residue numbers are indicated by a scale (written as 10,20,30 ..) above the sequence. The first row (AA) is amino acid sequence as submitted by the user. The remaining 4 rows provides the location of predicted turns. Predicted turn residues are indicated as 4 residues block denoted by symbol *. Four different rows or frames (F1, F2, F3 & F4) are considered to account for overlapping beta-turns.
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AA HKFLDSFDEPDLFIRDEKFDISTWEIARFCNVMHDSKFLYQWIEDPWQDSWQDEIWDE
F1 ----********---------------------****-------********------
F2 ----------------------------------****--------****--------
F3 -----------------------------------------------****-------
F4 ----------------------------------------------------------
A ß-turn is four residues long. Suppose a ß-turn is predicted between residues 34 and 37 and another turn is predicted between residues 35 and 38 (as in the example above). To display these overlapping turns, the concept of different frames is used. So, in this case the turn between residue 34 and 37 is displayed in frame 1st (F1) and the turn between residues 35 and 38 is displayed in frame 2nd (F2) and so forth. So, in 1st frame (F1) the turns are predicted from position 1 to 4, 5 to 8, 9 to 12 and so on. For 2nd frame (F2), turns are predicted from position 2 to 5, 6 to 9 and so on . Similarly, we do for frames 3rd (F3) and 4th (F4).
Nomenclature
The graphical (non-frames) output consist of 2 rows. The first row (AA) is the amino acid sequence as submitted by the user. The second row gives the location of predicted beta-turns denoted by symbol *. Overlapping turns are displayed in one frame only. The following figure shows the turns as located by a particular method. In non-graphical frame all these turns will be displayed in one row/frame only. As shown below, the turn HDSK at position 34-37 and the turn DSKF at position 35-38 are displayed in one frame only.
Predicted location of ß-turns
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AA HKFLDSFDEPDLFIRDEKFDISTWEIARFCNVMHDSKFLYQWIEDPWQDSWQDEIWDE
S.No Turn Position
1 DSFD 5-8
2 EPDL 9-12
3 HDSK 34-37
4 DSKF 35-38
5 DPWQ 45-48
6 WQDS 47-50
7 QDSW 48-51
8 DSWQ 49-52
Non-graphical output:
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AA HKFLDSFDEPDLFIRDEKFDISTWEIARFCNVMHDSKFLYQWIEDPWQDSWQDEIWDE
----********---------------------*****------********------
Sample output for method of prediction = "All"
A consensus method can be developed by combining all the algorithms.Users can predict beta-turns in the query sequence by simultaneously using all the mentioned methods and can determine those segments in the sequence that are predicted as beta-turns by all the methods (i.e., the consensus sequence) and all such segments will be marked in 'purple' color (as shown below, the consensus sequence DSKF) while rest of the sequence will be in brown color. An output example is given below:
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HKFLDSFDEPDLFIRDEKFDISTWEIARFCNVMH
LYQWIEDPWQDSWQDEIWDE
Chou-Fasman algorithm -------****---------------------*****------********------
Thornton's frequencies ----****----------******---------****------********------
GORBTURN (v3.0) ************-------******---------****------********------
Correlation model ----********--------------******--****--------------------
Sequence coupled model ---*********-****--------****--*********************------
Here, in the example above the DSKF sequence is predicted as ß-turn by all the methods.
Help for advanced prediction
In advanced prediction, the program identifies the residues in the query sequence that are present in ß-turn (the ß-turn location) and also identifies the ß-turn type (the ß-turn classification). Only 2 methods (Thornton's positional frequencies and GORBTURN (v3.0)) can provide the classification. Moreover, in advanced prediction, the program provide the choice for cut-off values.
Thornton's positional frequencies
Nomenclature
AA = the amino acid sequence (as submitted by user)
S. No. = serial numbers of the predicted turns
Turn = amino acid sequence of the segment forming the turn
Position = position number of the residues in the turn
Turn type = type of turn-Type I or Type II
Residue numbers are indicated by a scale above the sequence (written as 10,20,30 ...).
Predicted location of ß-turns
10 20 30 40 50
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AA FGDSHFKDSPKGLMNDDPEDGHKFHDTYIREYASLKPMNGDFERWETGHRDY
S.No Turn Position Turn type
1 DSHF 3-6 I
2 SPKG 9-12 I
3 LMND 13-16 II
4 DPED 17-20 I
5 PEDG 18-21 I
6 HDTY 25-28 I
7 PMNG 37-40 II
8 MNGD 38-41 II
9 NGDF 39-42 I
10 WETG 45-48 I
11 HRDY 49-52 I
Nomenclature
AA = the amino acid sequence (as submitted by user)
F1 = first frame
F2 = second frame
F3 = third frame
F4 = third frame
Residue numbers are indicated by a scale above the sequence (written as 10,20,30 ...).
Type-I turns are shown in green stars.
Type-II turns are shown in red stars.
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AA FGDSHFKDSPKGLMNDDPEDGHKFHDTYIREYASLKPMNGDFERWETGHRDY
F1 --****--************----****--------****----********
F2 -----------------****----------------****-----------
F3 --------------------------------------****----------
F4 ----------------------------------------------------
GORBTURN (v3.0)
Nomenclature
AA = the amino acid sequence (as submitted by user)
S. No. = serial numbers of the predicted turns
Turn = amino acid sequence of the segment forming the turn
Position = position number of the residues in the turn
Turn type = Type I, II, I', II',VIII & non-specific(NS)
Residue numbers are indicated by a scale above the sequence (written as 10,20,30 ...).
Predicted location of ß-turns
10 20 30 40 50
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AA FGDSHFKDSPKGLMNDDPEDGHKFHDTYIREYASLKPMNGDFERWETGHRDY
S.No Turn Position Turn type
1 DSHF 3-6 I
2 FKDS 6-9 NS
3 SPKG 9-12 I
4 NDDP 15-18 VIII
5 DPED 17-20 I
6 PEDG 18-21 I
7 DGHK 20-23 NS
8 FHDT 24-27 NS
9 PMNG 37-40 I
Nomenclature
Sequence = amino acid sequence as submitted by the user
Helix/sheet = helix and sheet prediction at each residue position is indicated by H and E respectively.
B-turn = turn predictions are indicated as 4 residue blocks with the turn type indicated by roman numerals (I, II, I', II', VIII & NS) where NS is non-specific ß-turn type.
A sample output is shown below:
Query seq
GORBTURN PREDICTION OF B-TURNS
------------------------------
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Sequence FGDSHFKDSPKGLMNDDPEDGHKFHDTYIREYASLKPMNGDFERWETGHR
Helix/Sheet H HH HHHHH
B-turn |_|__| |__| |__| |__||__| |__|
B-turn II I I VIII NS NS I
B-turn |__| |__|
B-turn NS I
B-turn |__|
B-turn I
B-turn
B-turn
--------------------------------------------------
| | | | | 100
Sequence DY
Helix/Sheet
B-turn
B-turn
B-turn
B-turn
B-turn
B-turn
B-turn
B-turn
--------------------------------------------------
