Click on the menu at the left to see which of the following sequence input methods are available.
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.
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.
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Select an available sequence database from this menu.

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

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

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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.

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

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List of peptides with modifications. These can be in three formats:

psm: Tab-delimited Peptide-Spectrum Match file.

prealigned: List of fixed width peptides centered around modification site separated by new lines.

fasta: List of fixed width peptides centered around modification site in FASTA format.

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Protein database to use for flanking information and background sequences in FASTA format.

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Minimum occurrences of modification required to output a motif. This threshold is applied after filter and eliminate repeats (if applicable).

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Motif width

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Create one motif per mass instead of one motif per mass and central peptide.

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Remove duplicate copies of modifications with identical flanking sequences for a user specified width.

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Filter PSMs using for a field specified within the uploaded file.

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Choose the algorithm used for searching motifs.

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Data Submission Form

Perform motif discovery on peptide-spectrum matches.

Choose an algorithm

Input the modification files

Enter the files with post-translational modifications (PTMs) for generating motifs.

PTM File Format: Sequence Column Name:

Input the flanking sequences

Enter sequences containing the flanking regions of matches.


Total Number of PTMs in Files 0
Total Number of PTM Types 0

Input job details

(Optional) Enter your email address.

(Optional) Enter a job description.

Advanced options hidden modifications! [Reset]

Filter Sequences?

Filter?Field Threshold 

How many occurrences are required?

How wide can motifs be?

Create single motif per mass?

Eliminate repeats

Warning: Your maximum job quota has been reached! You will need to wait until one of your jobs completes or 1 second has elapsed before submitting another job.

This server has the job quota set to 10 unfinished jobs every 1 hour.

Note: if the combined form inputs exceed 80MB the job will be rejected.