SSA

Signal Search Analysis Server

Optimization of a Locally Over-Represented Sequence Motif

Background: Input is a set of DNA sequences adjacent or around a functional site plus a sequence motif defined by a consensus sequence or a weight matrix. The input sequence motif serves as an initial model for starting the optimization process. The output is a complete weight matrix-based description of a sequence motif maximizing a quantitative criterion of local over-representation, including the optimized border positions and cut-off value.
A detailed description of the method can be found here
Sequence Input
Transcription initiation sites
Translation initiation sites
Sequence input via server-resident FPS file(s)
       Name(s) of FPS file(s) (up to four):
Upload Sequence Set (in Fasta Format)


Internal position of functional site :
Upload FPS File


FPS name :

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: max. gap: min. chi-squared:

Minimal relative entropy:

Maximal false-positive rate (%)
Normalization mode:     mononucleotide     dinucleotide
Initial cut-off optimization:     yes     no

Smoothing %     Maximal # cycles

Signal Description
From Library      
Consensus sequence
Weight matrix
  Name (max. 20 chars):
  Reference position:
  Cut-off value: absolute       percentage       mismatches
  

 

Last update 13 Jul. 2010