SSA

Signal Search Analysis Server

Generation of a Signal List

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 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 :
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)

 

Last update 13 Jul. 2010