If your sequences are not in a standard alphabet (DNA, RNA or protein), you must input a custom alphabet file.

Type in sequences

When this option is available you may directly input multiple sequences by typing them. Sequences must be input in FASTA format.

Upload sequences

When this option is available you may upload a file containing sequences in FASTA format.

Upload BED file

When this option is available you may upload a file containing sequence coordinates in BED format.

Databases (select category)

When this option is available you may first select a category of sequence database from the list below it. Two additional menus will then appear where you can select the particular database and version desired, respectively. The full list of available sequence databases and their descriptions can be viewed HERE.

Submitted sequences

This option is only available when you have invoked the current program by clicking on a button in the output report of a different MEME Suite program. By selecting this option you will input the sequences sent by that program.

Specify a file to upload containing sequence coordinates in BED format. The file must be based on the exact genome version you specified in the menus above.

Select an available sequence database from this menu.

Select an available version of the sequence database from this menu.

Select an available tissue/cell-specificity from this menu.

Selecting this option will filter the sequence menu to only contain databases that have additional information that is specific to a tissue or cell line.

This option causes MEME Suite to use tissue/cell-specific information (typically from DNase I or histone modification ChIP-seq data) encoded as a position specific prior that has been created by the MEME Suite create-priors utility. You can see a description of the sequence databases for which we provide tissue/cell-specific priors here.

Note that you cannot upload or type in your own sequences when tissue/cell-specific scanning is selected.

Enter the email address where you want the job notification email to be sent. Please check that this is a valid email address!

The notification email will include a link to your job results.

Note: You can also access your jobs via the Recent Jobs menu on the left of all MEME Suite input pages. That menu only keeps track of jobs submitted during the current session of your internet browser.

Note: Most MEME Suite servers only store results for a couple of days. So be sure to download any results you wish to keep.

Enter text naming or describing this analysis. The job description will be included in the notification email you receive and in the job output.

DREME looks for motifs that are enriched in your sequences relative to a control set of sequences.

By default DREME creates the control set by shuffling each of your sequences, conserving dinucleotide frequencies ("Shuffled input sequences").

Alternatively, you may may provide a set of control sequences ("User-provided sequences").

IMPORTANT: If you provide the control sequences, they should have exactly the same length distribution as the the primary sequences. (E.g., all sequences in both sets could have the same length, or for each sequence in the primary set there could be exactly N sequences with the same length as it in in the control set.) Failure to ensure this may cause DREME to fail to find motifs or to report inaccurate E-values.

Select a file of FASTA formatted nucleotide sequences or paste in actual FASTA formatted nucleotide sequences to search for small regular expression motifs.

DREME works best with sequences which are less than 500 nucleotides long so if you have very long sequences DREME might work better if you split long sequences into shorter ones. For ChIP-seq we recommend using sequences of length 100 centered on the summit or center of the peak. The more sequences that you can give DREME the more subtle the motifs it can find.

See the example DNA sequences which were used to create the sample output to get an idea of input that works well for DREME.

Input comparative sequences which have approximately the same length distribution and background frequencies but which are unlikely to contain the motifs that you are attempting to find.

Note that using comparative sequences that are much longer or shorter than your input sequences has the potential to create incorrect p-values.

Enter the email address where you want the job notification email to be sent. Please check that this is a valid email address!

The notification email will include a link to your job results.

Note: You can also access your jobs via the Recent Jobs menu on the left of all MEME Suite input pages. That menu only keeps track of jobs submitted during the current session of your internet browser.

Note: Most MEME Suite servers only store results for a couple of days. So be sure to download any results you wish to keep.

The job description will be included in the notification email you receive and in the DREME output.

DREME stops looking for motifs when one of these limits is met. There is an additional time limit which is set by the server operator.

E-value threshold

The expected number of false positives. This may be any positive number. DREME stops if a motif is found whose E-value exceeds this threshold.

Number of motifs

DREME stops if it has found this many motifs. By default DREME does not limit the number of motifs to be found.

Checking this box instructs DREME to NOT check the reverse complement of the input sequences for motif sites when reading sequences.

Note: When your sequences are RNA, you should select this option to ensure that only the given strand is searched for motifs.