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Signal Search Analysis Server

Generation of a Constraint Profile : Input Form

Method Description: 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 frequencies of a collection of sequence motifs contained in a signal sequence collections. The signal sequence collection may for instance consist of all tetranucleotides consensus sequences with one mismatch allowed. The output is a so-called "constraint profiles", a graph showing the non-randomness in the distribution of the motifs as a function of the position relative to the functional site. 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 :
Retrieve graph in :
Color   Greyscale

 

 

Signal collection :
complete :
# of bases
random :
# of bases
# of signals
# random number seed (from 0. to 1.)
special:
# of bases
# total length
Title (max. 10 characters) :
List signal types in text area below.

Min. # of matches: (optional, reasonable default value supplied by program)

Questions and comments regarding this method should be sent to: Philipp Bucher;
Bug reports should be sent to: Giovanna Ambrosini;

References:

  1. Bucher P, Trifonov EN (2000), Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res. 14, 10009-10026