Optimization of a Locally Over-Represented Sequence Motif

SSA Input Data
Select available Data Sets
         Genome :   
         Data Type :   
         Series :   
         Sample :   

Sequence input via server-resident FPS file(s)
        Name(s) of FPS file(s) (up to four):
        Feature  :

Upload Sequence Set in Fasta Format

Internal position of functional site :

Functional Position Set (FPS) name :

FPS type (e.g. TSS) :

Upload custom Data
      from a FILE (gzip or zip formats are also accepted):
      or from a URL:
      Experiment  :
      Feature  :
Additional Input Data Options
 Repeat Masker      
Sequence Range
Entire sequence range (for uploaded sequences only)

5' border:       3' border:
Optimization parameters
Window size: min.         max.         increment
Cut-off %: min. %    max. %    increment
Search mode: forward     bidirectional
Selection mode: single best     non-overlapping     all
Context range: left border     right border
Matrix extension: yes     no

          max. gap       min. chi-sqr    
          Minimal relative entropy    

Maximal false-positive rate (%):
Normalization mode: mononucleotide     dinucleotide
Initial cut-off optimization: yes     no
Smoothing %:
Maximal # cycles:
Shuffling sequences
Region size   :         
Signal Description
PWMs from Library     
        Motif Library:  
        Motif :  
Custom Weight Matrix
        PWM text  


absolute    percentage    p-value
  Bg base composition

Consensus seq


  Name (max 20 chars)
  Reference position
Retrieve graph in :

Color    Greyscale




Last update October 2017