The name of the motif uses the IUPAC codes for nucleotides or proteins.
Letters representing multiple nucleotides are used in nucleotide motif
positions where several nucleotides are favored.
The name of the motif is <index>-<consensus>,
where <index> is the order in which the motif was found,
and <consensus> is an approximation of the motif
by an IUPAC sequence.
The logo of the reverse complement motif.
The rules for construction logos are given in
the Description section of the documentation for the MEME Suite utility
ceqlogo.
Submit your motif to another MEME Suite program (see list below), or Download your motif
as a probability matrix, count matrix or MEME formatted motif, or download
a Sequence Logo for your motif.
Supported Programs
Tomtom
Tomtom is a tool for searching for similar known motifs.
MAST
MAST is a tool for searching biological sequence databases for
sequences that contain one or more of a group of known motifs.
FIMO
FIMO is a tool for searching biological sequence databases for
sequences that contain one or more known motifs.
GOMo
GOMo is a tool for identifying possible roles (Gene Ontology
terms) for DNA binding motifs.
SpaMo
SpaMo is a tool for inferring possible transcription factor
complexes by finding motifs with enriched spacings.
The Score is the unadjusted p-value of the motif based on the appropriate test
applied to the training set sequences.
Since the Score is not adjusted for multiple tests, it cannot
be used to determine the statistical significance of the motif.
The Score is used by STREME to select the best motif at each iteration.
For determining if a motif is statistically significant, you should use the
value in the P-value column. If there is no P-value column, that
means that the positive hold-out set would have been too small (fewer than 5 sequences).
For very small sequence sets, it is not practical for STREME to compute an accurate p-value.
In that case, you can determine if your motif is significant by running STREME twenty or more
times on shuffled versions of your positive dataset,
and seeing if the Score is always larger than the Score using the original sequences.
You can make shuffled sequence datasets using the MEME Suite command-line utility
fasta-shuffle-letters) if you
have installed the MEME Suite on your own computer.
The statistical test used in computing the Score is either the Fisher Exact Test,
the Binomial Test, or the Cumulative Bates distribution. (See Inputs and Settings
for the particular test being used.) The Fisher Exact Test and the Binomial Test both
measure the enrichment of the motif in the positive test sequences compared to the
the negative test sequences.
(The Binomial Test is used when the positive and negative sequences have different average lengths.)
The Cumulative Bates distribution measures the tendency
of motif to be near the center of the sequences.
The p-value of the motif based on applying the appropriate statistical test
to the test set sequences. The p-value is an accurate estimate of
the statistical significance of the motif as long as the length
distributions of the positive and negative sequences are the same.
The statistical test used in computing the p-value is either the Fisher Exact Test,
the Binomial Test, or the Cumulative Bates distribution. (See Inputs and Settings
at the bottom of this document for the particular test being used.)
The Fisher Exact Test and the Binomial Test both
measure the enrichment of the motif in the positive test sequences compared to the
the negative test sequences.
(The Binomial Test is used when the positive and negative sequences have different average lengths.)
The Cumulative Bates distribution measures the tendency
of motif to be near the center of the sequences.
The score threshold for determining if a potential site is a match
to the motif. The same threshold is applied when determining matches in
the training and test sequences. The threshold is in bits.
The match score of a position in a sequence is determined by converting
the motif to a base-2 log-odds matrix using the formula log2(prob[a][i]/background[a]).
Here, prob[a][i] is the probability of the letter 'a' at position 'i' of the motif,
and background[a] is the probability of the letter 'a' according to the background.
The name of the file containing the negative (e.g., control)
sequences relative to which STREME will look for motifs enriched
in the positive sequences, or the words "n-Order Shuffled Sequences" if
no negative sequence file was given and the negative sequences are
shuffled copies of the positive sequences.
0-order shuffling preserves 1-mer frequencies (i.e., the letter frequencies),
1-order shuffling preserves 2-mer frequencies, etc.
If you use STREME in your research please cite the following paper:
Timothy L. Bailey,
"STREME: Accurate and versatile sequence motif discovery",
bioRxiv, preprint, 2020.
