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Signal Search Analysis Server

Generation of a Signal Occurrence Profile : Input Form

Background: A set of fixed-length DNA sequences aligned with respect to a functional site, e.g. a transcription start site, is scanned in a sliding window in order to determine the occurrence frequency of a particular sequence motif (signal) defined by a particular signal. Multiple sets can be processed at the same time. The output is a graph showing the occurrence frequency of the signal as a function of its position relative to the functional sites.
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 :

Functional site type :

Functional position set (FPS) name :
Sequence range :
Entire sequence range (for uploaded sequences only)

5' border:       3' border:
Sliding window parameters:
Window size:       Window shift:
Search mode:       forward    bidirectional
Retrieve graph in :
Color    Greyscale
Signal description:
From Library      
Consensus sequence
OR
Weight matrix
Name (max. 20 characters):

Reference position:
Cut-off value:
absolute       percentage       mismatches   
References:
  1. Bucher P, Trifonov EN (1986), Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res. 14, 10009-10026
Questions and comments regarding this method should be sent to: Philipp Bucher;

Bug reports should be sent to: Giovanna Ambrosini;