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This is a web server that enables the analysis of multiple DNA sequences using sets of Position Weight Matrices from the JASPAR and TRANSFAC™ databases, using multiple scanning algorithms. (The use of the TRANSFAC matrices for analyses is free for users from non-profit organizations only. Commercial users have to license the TRANSFAC database [Disclaimer].)

Help on using this server can be found by clicking on the linked features within the page and using the FAQ.

Species Matrices
Upload sequence(s) in Fasta format

Limits: 50 sequences or 50K bps.
Clover max. individual sequence length 5K bps.

Stringent MotifLocator Scans 0.1% 0.05% 0.01%
Multi Algorithm Scans
Clover 

P-value Threshold 
Score Threshold 
Pseudocount  		MotifLocator 

Motif Threshold 
  		MotifScanner 

Prior Probability 
 

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The development of MotifMogul is supported by a grant from the National Institute of Allergy and Infectious Disease (NIAID), a division of the National Institutes of Health (NIH).
Server Version: 1.0 November 2006