MEME -- Multiple EM for Motif Elicitation

Motif discovery tool

  • motif distribution
    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.
  • number of motifs
    MEME will look for up to this number of distinct motifs in the training set. MEME will stop when this number of motifs has been found, or when none can be found with E-value less than 10000.
  • number of sites[optional]
    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.
    For example, if you know that each motif is likely to occur at least 5 times but no more than 8 times in the training set, you could specify:
    Minimum sites = 5
    Maximum sites = 8
    MEME will then only report motifs with between 5 and 8 occurrences, inclusive, in the training set. (The same range [5,...,8] will apply, separately, to each motif MEME finds.) MEME may still find motifs with slightly fewer or more occurrences then those you specify. In the above example, if there is a motif in the training set with only 4 occurrences, MEME may still find it, but it will report 5 occurrences, one of which will be erroneous. Likewise, if a motif in the training set has 9 occurrences, MEME will probably still find it, but it will report only 8 of its occurrences.
    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 blank.
    Note 1:
    Leave these fields blank if you have selected "One per sequence" in the "How you think the occurrences... are distributed" field. In that case, each sequence must have exactly one occurrence of each motif. It also doesn't make any sense to set the maximum number of sites to a number larger than the number of sequences if you have chosen the "Zero or one per sequence distribution. In that case, there can never be more occurrences of a motif than there are sequences.
    Note 2:
    These fields are optional. If you leave them blank, MEME will choose limits depending on the type of occurrence distribution you have specified and the number of sequences (n) in the training set. MEME will also override your settings if they conflict with the type of distribution you have chosen (see Note 1, above).
    Default Numbers of Sites for each Motif
    type of distribution minimum sites maximum sites
    one occurrence per sequence n n
    zero or one occurrence per sequence sqrt(n) n
    any number of repetitions per sequence sqrt(n) min(5*n, 50)
  • motif width
    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.
    Note on maximum width:
    Both protein and DNA motifs are often shorter than the default "maximum width" (50). It is often advisable for you to reduce that parameter to a much smaller value (e.g., in the range 10--20) by entering a new value in the box.
  • use a different Markov background model
    You can provide a Markov background model for MEME to use as its model of "random" sequences. The format and effect of the background model file is described under the topic "BACKGROUND MODEL" on the MEME "man page".
    The downloadable version of MEME contains a script named "fasta-get-markov" that you can use to create background model files in the correct format from FASTA sequence files.
  • search given strand only
    MEME searches for motifs on both the given DNA strand and the reverse complement strand by default. Checking this box will cause MEME to search the given DNA strand only.
  • discriminative motif discovery
    Providing negative sequences using this option results in creation of a position-specific prior (PSP), with the negative sequences and the main (positive) sequences as inputs to a PSP generator program, which is run as an extra step before running MEME. The resulting PSP file is used as an additional input to MEME. For more detail, see documentation on discriminative motif discovery.
  • look for palindromes only
    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.