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.

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

By default STREME creates the control set by shuffling each of your sequences, conserving k-mer frequencies ("Shuffled input sequences"), where k=3 for DNA and RNA sequences, and k=1 for protein or custom alphabet sequences.

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

IMPORTANT NOTE: If you provide control sequences, they should have the same length distribution as your the primary sequences. For example, 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 STREME to report inaccurate estimates of the statistical significance (p-value) of the motifs it finds.

Select a file of FASTA formatted biological sequences or paste in FASTA formatted biological sequences to search sequence motifs.

The more sequences that you can give STREME the more subtle the motifs it can find. For ChIP-seq we recommend using sequences of length 100bp centered on the summit or center of the peak. For CLIP-seq we recommend using the actual peak regions.

The STREME webserver limits the total length of the sequences to 10,000,000 (DNA and RNA) and 1,000,000 (protein and custom alphabets).

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

Select a file of FASTA formatted biological sequences or paste in FASTA formatted biological sequences to use as controls in the search for motifs.

Your control sequences should have approximately the same length distribution and background frequencies as your primary sequences the motifs that you are attempting to find. The more control sequences that you can give STREME, the more subtle the motifs it can find.

The STREME webserver limits the total length of the control sequences to 10,000,000 (DNA and RNA) and 1,000,000 (protein and custom alphabets).

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 STREME output.

This is the width (number of characters in the sequence pattern) of a single motif. STREME chooses the optimal width of each motif individually using a heuristic function. You can choose limits for the minimum and maximum motif widths that STREME will consider. The width of each motif that STREME reports will lie within the limits you choose.

The background model normalizes for biased distribution of letters and groups of letters in your sequences. A 0-order model adjusts for single letter biases, a 1-order model adjusts for dimer biases (e.g., GC content in DNA sequences), etc.

By default STREME will determine the background Markov model from the control sequences (or from the primary sequences if you do not provide control sequences). The order of the background model depends on the sequence alphabet, but you can also set it manually (see option "What Markov order...", below). Alternately you may select "Upload background model" and input a file containing a background model.

The downloadable version of the MEME Suite contains a program named "fasta-get-markov" that you can use to create background model files in the correct format from FASTA sequence files.

Specify the order (m) for the background model and sequence shuffling. By default, STREME uses m=2 for DNA and RNA sequences, and m=0 for protein or custom alphabet sequences. Check this box and set the value of m if you want to override the default value of m that STREME uses.

If you upload a background model (see option above), STREME will only use the m-order portion of that model. If you do not upload a background model, STREME will create an order-m model from the control sequences that you provide, or from the shuffled primary sequences if you don't provide control sequences.

If you do not specify a set of control sequences, STREME will create one by shuffling each primary sequence while preserving the frequencies of all words of length k that it contains, where k=m+1.

If this option is checked, STREME will NOT trim the control sequences even if their average length exceeds that of the primary sequences. This will cause STREME to use the (less accurate) Binomial test rather than the Fisher Exact test if the control sequences are longer (on average) than the primary sequences.

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

p-value threshold

The probability of a motif being found that would discriminate the primary sequences from the control sequences at least as well, assuming that the letters in the primary sequences were randomly shuffled. STREME stops when 3 motifs have been found whose p-values exceed this threshold. If STREME is unable to estimate the p-values of motifs, it will stop when 5 motifs have been found.

Number of motifs

Check this box and set the (maximum) number of motifs you want STREME to find before it stops. STREME will ignore the p-value threshold if this box is checked. By default STREME does not limit the number of motifs to be found, but uses the p-value threshold as its stopping criterion.

When your sequences are in the DNA alphabet but you want them to be treated as single-stranded RNA, check this box.

For the site positional distribution diagrams, align the sequences on their left ends, on their centers, or on their right ends. For visualizing motif distributions, center alignment is ideal for ChIP-seq and similar data; right alignment for sequences upstream of transcription start sites; left alignment for many proteins or 3' UTR sequences.

When this option is selected, if the FASTA sequence header of an input sequence contains genomic coordinates in UCSC or Galaxy format the discovered motif sites will be output in genomic coordinates. If the sequence header does not contain valid coordinates, the sites will be output with the start of the sequences as position 1.