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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. Upload sequences When this option is available you may upload a file containing sequences in. 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. 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.
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By selecting this option you will input the sequences sent by that program. 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 that has been created by the MEME Suite utility. You can see a description of the sequence databases for which we provide tissue/cell-specific priors. 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!
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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. Classic mode You provide one set of sequences and MEME discovers motifs enriched in this set. Enrichment is measured relative to a (higher order) random model based on frequencies of the letters in your sequences, or relative to the frequencies given in a 'Custom background model' that you may provide (see Advanced options). Discriminative mode You provide two sets of sequences and MEME discovers motifs that are enriched in the first (primary) set relative to the second (control) set. In Discriminative mode, we first calculate a from the two sets of sequences. MEME then searches the first set of sequences for motifs using the position-specific prior to inform the search. This approach is based on the simple discriminative prior 'D' described in Section 3.5 of.
We modify their approach to search for the 'best' initial motif width, and to handle protein sequences using. 
Refer to the documentation and to for more details. Differential Enrichment mode You provide two sets of sequences and MEME discovers motifs that are enriched in the first (primary) set relative to the second (control) set. In Differential Enrichment mode, MEME optimizes an objective function based on the hypergeometric distribution to determine the relative enrichment of sites in the primary sequences compared to the control sequences.
Spaced triples are sub-sequences in which only the first and last letter (residue or amino acid for protein) and one interior letter are used in matches. For example, the subsequence MTFEKI contains the following triples: MT.I M.F.I M.E.I M.KI where '.' Matches anything. We use spaced triples for protein because the probability of exact matches is much lower than for DNA due to the much larger amino acid alphabet. To score a word using spaced triples, we count how often each triple contained in the word occurs in the primary and control sequence sets, and use the maximum over all triples as the word count in the formula for scoring words described. Please enter sequences that you believe contain patterns you wish to avoid making motifs from. This set of sequences is referred to as the 'control sequence set.