Online Motif Discovery with WebMOTIFS

WebMOTIFS is an online tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs to search for DNA-sequence motifs, and to easily combine and evaluate the results.

WebMOTIFS is a combination of two tools, TAMO and THEME. TAMO runs a number of motif discovery programs on input sequences, then combines, analyzes, and clusters the results. TAMO incorporates the motif discovery programs AlignACE, MDscan, MEME, and Weeder. We gratefully acknowledge the authors of these programs. THEME does Bayesian motif analysis, incorporating prior knowledge about likely motifs. The graphic below explained the basic motif discovery and post-processing offered by WebMOTIFS; you can run Bayesian motif discovery on your input list of coregulated genes as well.

We gratefully acknowledge the authors of AlignACE, MDscan, MEME, and Weeder for permission to include their programs in WebMOTIFS.

Please note that users of WebMOTIFS may be bound by the user agreements of these programs. Click here for details.

Commercial and clinical use of WebMOTIFS is prohibited.

Try out WebMOTIFS!

User input							How to give input (genes and seeds) Table of gene/probe nanes
Seeds		Coregulated genes
Bayesian Motif Discovery		De novo Motif Discovery					MD program details Intermediate output format
							Scoring and significance testing details
							Clustering Method
	Final Output						Sample final output, annotated

WebMOTIFS References:

Romer KA, Kayombya GR, Fraenkel E. "WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches." Nucleic Acids Research. 2007 June 21. Article Full Text

WebMOTIFS is based on the TAMO software package:
Gordon DB, Nekludova L, McCallum S, Fraenkel E. "TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs." Bioinformatics. 2005 May 19; 21(14):3164-3165.
You can find more documentation on TAMO, and download the software package, at http://fraenkel.mit.edu/TAMO/.

Questions or comments? Please email tamo@mit.edu.