WebMOTIFS: Job submission

Welcome to WebMOTIFS, a web interface to TAMO and THEME. You can use this form to submit basic motif discovery jobs, using MDscan, AlignACE, Weeder, and MEME to find motifs in unaligned sequences from S. cerevisiae, M. musculus, and H. sapiens. At the same time, you can do Bayesian motif discovery using THEME. We will run your jobs and email you with the location of the results. We hope to have more motif discovery programs and genomes available soon.

We gratefully acknowledge the authors of AlignACE, MDscan, MEME, and Weeder. Plase note that users of WebMOTIFS may be bound by copyrights and user agreements of these programs. See here for details.

Commercial and clinical use of WebMOTIFS is prohibited.

Please email tamo@mit.edu with any problems, and we will fix them as soon as possible. If you've had problems in the past, please look at the bug-fix log for a record of problems that have been resolved.

Click here for an overview of WebMOTIF. Click here for an explanation of the format your results will take.

We occasionally send out news of updates to WebMOTIF. If you wish to receive these messages, please check this box.

Query
Email address:
Job name:

Input
Organism
Name type:	Please note that analyzing longer sequences increases running time.
Gene/probe names: or	Please provide at least 10 gene/probe names.
Gene/probe names file (plain text):

Methods

for motif discovery

Basic

(sequence information only)

AlignACE (medium)
MEME (slow)

MDscan (fast)
Weeder (medium)

	Expected Motif Length
	Less than 10 nucleotides Less than 12 nucleotides Less than 14 nucleotides
	Significance Testing

*Advanced*	(Bayesian, incorporating binding domain information)
	THEME
		Initial Hypotheses
		Try all initial hypotheses
:		AP2-domain bZIP (Basic Leucine Zipper) bZIP_MAF (Basic Leucine Zipper/MAF Extended Homology Region) CBFB_NFYA (CCAAT-binding transcription factor subunit B) CTF_NFI (CCAAT-box-binding factor/Nuclear Factor I) CUT E2F_TDP (E2F/DP family winged helix) Ets (Erythroblast Transformation Specific Domain) Fork_head GATA HALZ (Homeobox associated leucine zipper) HLH (Helix-loop-helix) HMG_box (High Mobility Group box) HNF-1_N (Hepatocyte nuclear factor 1, N term.) homeobox HSF_DNA-bind (Heat Shock Factor-type DNA binding domain) IRF (Interferon regulatory factor) MH1 (MAD homology 1 domain)	myb_DNA-binding (Myb-like DNA-binding domain) Myc_N_term (Myc N-terminal) PAX (Paired box) PBX (PBC) pou RFX_DNA_binding (Regulatory Factor binding to X box DNA-binding domain) RHD (Rel Homology Domain) Runt SRF-TF (Serum Response Factor-type) STAT_bind (Signal Transducers and Activators of Transcription protein DNA-binding domain) TBP (Transcription Factor TFIID/TATA-binding protein) TEA (Transcriptional Enhancer Activators/ATTS domain family) TF_AP-2 (Transcription Factor Activator Protein 2) TF_Otx (Otx1 Transcription Factor) WRKY zf-C4 (Zinc finger, C4 type/Nuclear Hormone Receptor) zf-Dof (Dof domain, Zinc finger) Zn_clus (Fungal Zn(2)-Cys(6) binuclear cluster domain)

Note that it may take a little while (sometimes up to 30 seconds or 1 minute) to check that your input is valid. Once your input has been checked, you will be re-directed to a page confirming your submission. Please do not click "Submit Query" multiple times.

Questions, comments, or bug reports? Please email tamo@mit.edu.

Website created by Katherine Romer, MIT class of 2008
Last updated 9/15/2006