Select a file of FASTA formatted DNA sequences or paste in actual FASTA formatted DNA sequences to find motifs.

See the sample sequences to get an idea of input that works well for MEME-ChIP.

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MEME-ChIP will compare any found motifs to this set and also check if any are centrally enriched.

MEME-ChIP can use databases installed on the server or search a user uploaded database in MEME DNA motif format by selecting the "Upload Your Own Database" option. For more information browse the supported databases.

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An uploaded database is a normal MEME DNA motif file with lots of motifs. The uploaded database must be smaller than 5MB.

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The job description will be included in the notification email you receive and in the MEME-ChIP output.

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When using the RNA sequences you should select this option to ensure that only the given strand is scanned for motifs.

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By default MEME-ChIP will determine the background Markov model from the provided sequences. Alternately a file containing a background model may be input here.

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

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This is where you tell MEME how you believe occurrences of the motifs are distributed among the sequences. Selecting the correct type of distribution improves the sensitivity and quality of the motif search.

Zero or one occurrence per sequence
MEME assumes that each sequence may contain at most one occurrence of each motif. This option is useful when you suspect that some motifs may be missing from some of the sequences. In that case, the motifs found will be more accurate than using the one occurrence per sequence option. This option takes more computer time than the one occurrence per sequence option (about twice as much) and is slightly less sensitive to weak motifs present in all of the sequences.
One occurrence per sequence
MEME assumes that each sequence in the dataset contains exactly one occurrence of each motif. This option is the fastest and most sensitive but the motifs returned by MEME may be "blurry" if any of the sequences is missing them.
Any number of repetitions
MEME assumes each sequence may contain any number of non-overlapping occurrences of each motif. This option is useful when you suspect that motifs repeat multiple times within a single sequence. In that case, the motifs found will be much more accurate than using one of the other options. This option can also be used to discover repeats within a single sequence. This option takes much more computer time than the one occurrence per sequence option (about ten times as much) and is somewhat less sensitive to weak motifs which do not repeat within a single sequence than the other two options.
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MEME will keep searching until it finds this many motifs or it hits some other threshold like the maximum run time. Note that MEME does not use an E-value threhold like DREME so you should always check the E-value of any found motifs.

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

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This is the total number of sites in the training set where a single motif occurs. You can choose different limits for the minimum and maximum number of occurrences that MEME will consider. If you have prior knowledge about the number of occurrences that motifs have in your training set, limiting MEME's search in this way can can increase the likelihood of MEME finding true motifs.

MEME chooses the number of occurrences to report for each motif by optimizing a statistical heuristic function, restricting the number of occurrences to the range you give here, or using defaults described below if you leave these fields deselected.

Zero or one occurrence per sequencesqrt(n)n
One occurrence per sequencenn
Any number of repetitionssqrt(n)min(5*n, 600)
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Checking this box causes MEME to search only for DNA palindromes. This causes MEME to average the letter frequencies in corresponding motif columns together. For instance, if the width of the motif is 10, columns 1 and 10, 2 and 9, 3 and 8, etc., are averaged together. The averaging combines the frequency of A in one column with T in the other, and the frequency of C in one column with G in the other. If this box is not checked, the columns are not averaged together.

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DREME will keep finding motifs until it hits one of the limits.

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Specify a minimum score for a match to be considered. If a sequence does not have any matches which meet this minimum score for a given motif, then that sequence will not be considered for that motif.

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This option limits the maximum region size that CentriMo will test. This option is useful if you have sequences longer than the normal 500bp and can help cut-down the multiple testing correction. When this option is not supplied CentriMo will test region sizes up to one less than the maximum number of places that a given motif can align to the sequence.

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This is the E-value threshold CentriMo uses for reporting enriched central regions for motifs. If multiple enriched regions overlap then the region with the best p-value and smallest size will be output.

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This option causes all regions up to the maximum region size to be considered even if they are not in the center. This can be useful with non-symetric data.

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This option enables you to store the sequence identifies which have their best match in the best region for each motif. This option can potentially make the CentriMo output file size much larger.

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MEME-ChIP logo
Version 4.9.1

Use this form to submit DNA sequences to MEME-ChIP. MEME-ChIP is designed especially for discovering motifs in LARGE (50MB maximum) sets of short (around 500bp) DNA sequences centered on locations of interest such as those produced by ChIP-seq experiments.

Data Submission Form

Perform motif discovery and enrichment on large DNA datasets.

Input the sequences

Enter DNA sequences in which you want to find motifs


Input the motif database

Input job queue details

Enter your email address.

Re-enter your email address.

Optionally enter a job description.

Universal options hidden modifications! [Reset]

Scan both DNA strands?

Use a custom background?

MEME options hidden modifications! [Reset]

What is the expected motif site distribution?

How many motifs should MEME find?

What width motifs should MEME find?

How many sites per motif is acceptable?

Should MEME restrict the search to palindromes?

DREME options hidden modifications! [Reset]

How should DREME limit its search?

CentriMo options hidden modifications! [Reset]

Set a minimum acceptable match score (bits)

Set the maximum allowed width of central region

Set E-value threshold for reporting centrally enriched regions

Find uncentered regions

Include sequence IDs