SSA

Signal Search Analysis Server

Generation of a Signal Occurrence Profile

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 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:
Search mode:       forward    bidirectional
Signal Description
From Library     
Consensus sequence
Weight matrix
  Name (max. 20 chars):
  Reference position:
  Cut-off value: absolute       percentage       mismatches
  
Retrieve graph in :
Color    Greyscale

 

Last update 13 Jul. 2010