CPR

SSA

Signal Search Analysis Server

Generation of a Constraint Profile

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 Sequence Set (in Fasta Format)


Internal position of functional site :

Functional Position Set (FPS) name :

FPS type (e.g. TSS) :
Upload FPS File


FPS name :

FPS type (e.g. TSS) :

Sequence Range
Entire sequence range (for uploaded sequences only)

5' border:       3' border:
Sliding window parameters
Window size :       Window shift :
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)

Retrieve graph in :
Color    Greyscale

 

Last update 13 Jul. 2010