The statistical significance of the motif. MEME usually finds the most
statistically significant (low E-value) motifs first. It is unusual to
consider a motif with an E-value larger than 0.05 significant so, as an
additional indicator, MEME displays these partially transparent.
The E-value of a motif is based on its log likelihood ratio, width,
sites, the background letter frequencies (given in the command line
summary), and the size of the training set.
The E-value is an estimate of the expected number of motifs with the
given log likelihood ratio (or higher), and with the same width and site
count, that one would find in a similarly sized set of random
sequences (sequences where each position is independent and letters are
chosen according to the background letter frequencies).
Click on the blue symbol below to reveal options allowing you
to submit this motif to another MEME Suite motif analysis program, to download this
motif in various text formats, or to download a sequence "logo" of
this motif PNG or EPS format.
Supported Programs
Tomtom
Tomtom is a tool for searching for similar known motifs.
[manual]
MAST
MAST is a tool for searching biological sequence databases for
sequences that contain one or more of a group of known motifs.
[manual]
FIMO
FIMO is a tool for searching biological sequence databases for
sequences that contain one or more known motifs.
[manual]
GOMo
GOMo is a tool for identifying possible roles (Gene Ontology
terms) for DNA binding motifs.
[manual]
SpaMo
SpaMo is a tool for inferring possible transcription factor
complexes by finding motifs with enriched spacings.
[manual]
The log likelihood ratio of the motif.The log likelihood ratio is the
logarithm of the ratio of the probability of the occurrences of the motif
given the motif model (likelihood given the motif) versus their
probability given the background model (likelihood given the null model).
(Normally the background model is a 0-order Markov model using the
background letter frequencies, but higher order Markov models may be
specified via the -bfile option to MEME.).
The information content of the motif in bits. It is equal to the sum
of the uncorrected information content, R(), in the columns of the motif.
This is equal relative entropy of the motif relative to a uniform
background frequency model.
The position in the sequence where the motif site starts. If a motif
started right at the beginning of a sequence it would be described as
starting at position 1.
These are the motif sites predicted by MEME and used to build the motif.
These sites are shown in solid color and hovering the cursor
over a site will reveal details about the site. Only sequences
that contain a motif site are shown.
These are the motif sites predicted by MEME plus
any additional sites detected using a motif scanning
algorithm.
These MEME sites are shown in solid color and
additional scanned sites are shown in transparent color.
Hovering the cursor over a site will reveal details about the site.
Only sequences containing a predicted or scanned motif site are shown.
The scanned sites are predicted using a
log-odds scoring matrix constructed from the MEME sites.
Only scanned sites with position p-values less
than 0.0001 are shown.
These are the same sites as shown by selecting the
"Motif Sites + Scanned Sites" button except that all
sequences, including those with no sites, are included
in the diagram.
The combined match p-value is defined as the probability that a
random sequence (with the same length and conforming to the background)
would have position p-values such that the product is smaller
or equal to the value calculated for the sequence under test.
The position p-value is defined as the probability that a
random sequence (with the same length and conforming to the background)
would have a match to the motif under test with a score greater or equal
to the largest found in the sequence under test.
Hovering your mouse over a motif site in the motif location
block diagram will show its position p-value and other information
about the site.
Each block shows the position and strength of a motif
site. The height of a block gives an indication of the
significance of the site as taller blocks are more significant.
The height is calculated to be proportional to the negative
logarithm of the p-value of the site, truncated at
the height for a p-value of 1e-10.
For complementable alphabets (like DNA), sites on the
positive strand are shown above the line,
sites on the negative strand are shown below.
Placing the cursor
over a motif site will reveal more information about the site
including its position p-value. (See the help
for the p-value column for an explanation of position
p-values.)
If you use MEME in your research, please cite the following paper:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover motifs in biopolymers",
Proceedings of the Second International Conference on Intelligent Systems
for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
[pdf]
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover motifs in biopolymers",
Proceedings of the Second International Conference on Intelligent Systems
for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
|