SIB Home page

Computational Cancer Genomics

Swiss EMBnet node

ExPASy

ISREC

	Signal Search Analysis Server Generation of a Signal List : Input Form
Bakground: 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 sequences 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 list of signals which are over- or under represented in particular windows as compared to a random expectation. A detailed description of the method can be found here

Signal Search Analysis Server

Generation of a Signal List : Input Form

Bakground: 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 sequences 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 list of signals which are over- or under represented in particular windows as compared to a random expectation.
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 :

Sliding window parameters :

Window size : Window shift :

Selection criteria:

Occurrence frequency :
Calculation mode :
Selection mode :
St-dev cut-off :
Sort list by :

Signal collection :

complete :
# of bases
random :
# of bases
# of signals
# random number seed
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:

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