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Signal Search Analysis Server

Find Motifs around Functional Sites : Input Form

Background: A set of fixed-length sequences located at the same relative position with respect to a functional site (eg. a transcription start site) is scanned for occurrences of a given motif. The motif may be defined by a consensus sequence or a weight matrix. The search may be confined to a sub-region within the sequences supplied. The program returns either the sequences containing the motif, the sequences not containing the motif, or the sequence regions around the motif.
See the SSA Server User Manual for further detail.

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 search range :
Entire sequence range (for uploaded sequences only)

5' border:       3' border:
Sequence Selection and Search criteria:

Search mode:       forward    bidirectional
Sequence Selection mode :   
Signal Description:
From Library      
Consensus sequence
OR
Weight matrix
Name (max. 20 characters):

Reference position:
Cut-off value:
absolute       percentage       mismatches   
Sequence Output :
Retrieve sequences in : FASTA     FPS

Sequence extraction range around matches (FASTA only) :

5' border:       3' border:
     
References:
  1. Bucher P, Trifonov EN (1986), Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res. 14, 10009-10026
Questions and comments regarding this method should be sent to: Philipp Bucher;

Bug reports should be sent to: Giovanna Ambrosini;