Cister : Cis-element Cluster Finder

Paste a DNA sequence into the box or enter a GenBank identifier:

OR upload a DNA sequence from a file:
(Optional) Set subsequence From: To:

Choose a bunch of cis-elements:

TATA	Sp1	CRE	ERE	NF-1	E2F	Mef-2	Myf
CCAAT	AP-1	Ets	Myc	GATA	LSF	SRF	Tef

AND / OR enter your own cis-elements:
(Get cis-element matrices from TRANSFAC - free registration required)

AND / OR upload cis-elements from a file:

Parameters: (use the defaults if in doubt)
a average distance between motifs within a cluster
b average number of motifs in a cluster
g average distance between clusters
w half-width of sliding window for local base composition
Motif probability threshold
Pseudocount

Return to Zlab Gene Regulation Hub

Contact: Martin Frith
Last modified: Monday, 18-Feb-2008 20:39:06 EST