REPPER - Detecting regions with short gapless REPeats in protein sequences

 
It finds PERiodicities by Fourier Transform (FTwin) and internal homology analysis (REPwin). The exact locations of the periodic patterns are traced by a sliding window. The output is complemented by coiled coil prediction (COILS) and optionally by secondary structure prediction according to Jones (PSIPRED).
 

Input

Enter sequence or sequence alignment
or use an example sequence
or upload a local file
Select alignment format

 

Options

Input mode
 Use input as given   Run PSI-BLAST  
Window size
 
Periodicity range
Min   
Max  
Scale
 Kyte-Doolittle hydrophobicity   Standard Binary   own Scale  
I   W  
V   Y  
L   P  
F   H  
C   E  
M   Q  
A   D  
G   N  
T   K  
S   R  
FTwin threshold
 
REPwin threshold
 
COILS Parameters
 unweighted   weighted  
 MTIDK matrix   PDB matrix  
Run PSIPRED
 

Job Options

Job-ID
 (leave empty for automatic creation)
Send notification to (optional)
 

 
 
M.Gruber, J.Söding, and A.N.Lupas (2005) REPPER - repeats and their periodicities in fibrous proteins Nucl. Acids Res., 33(2), W239-43 FREE PDF