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Signal Search Analysis Server

Optimization of a Locally Over-Represented Sequence Motif: Input Form

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 the sequence (in Fasta Format)


Internal position of functional site :
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:
Normalization mode:     mononucleotide     dinucleotide

Smoothing %     Maximal # cycles

Signal description:
From Library      
Consensus sequence
OR
Weight matrix
Name (max. 20 characters):

Reference position:
Cut-off value:
absolute       percentage       mismatches   
Output options:
References:
  1. Bucher P (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578.
Questions and comments regarding this method should be sent to: Philipp Bucher;

Bug reports should be sent to: Giovanna Ambrosini;