Select this option if you have protein motifs but DNA sequences.
The DNA sequences will be translated on the fly to protein at each frame
for comparison with the motifs.
Select this option if you want MAST to remove any motifs that are
too similar to other motifs in your query. Having pairs of motifs
that are too similar will cause the E-values computed by MAST
to be inaccurate. If you don't select this option, problematic
motifs will be highlighted in your MAST output.
MAST only displays sequences matching your query with E-values
below the given threshold you specify here. By default, sequences in the
database with matches with E-values less than 10 are displayed.
If your motifs are very short or have low information content (are not
very specific), it may be impossible for any sequence to achieve a low
E-value. If your MAST search returns no hits, you may wish to increase
the E-value display threshold and repeat the search.
MAST can ignore motifs in the query with E-values above a
threshold you select. This is desirable because motifs with high
E-values are unlikely to be biologically significant. If this
option is disabled then MAST will use all the motifs in the query,
regardless of their E-values.
This option only works for motifs where the E-value is included
in the motif file. MAST does not have any capability for re-assessing the
signficance of a motif.
This option can improve search selectivity when erroneous matches are
due to biased sequence composition.
MAST normally computes E-values and p-values using a
random sequence model based on the overall letter composition of
the database being searched. Selecting this option will cause MAST
to use a different random model for each target sequence.
The random model for each target sequence will be based on its letter
composition, not that of the entire database.
Using this option will tend to give more accurate
E-values and increase the E-values of compositionally
biased sequences. This option may increase search times
substantially if used in conjunction with E-value display
thresholds over 10, since MAST must compute a new set of motif score
distributions for each high-scoring sequence.
MAST displays motifs that score above a threshold for all high-scoring
sequences. By default, this threshold is based on the probability of the
motifs without regard to the length of the sequence. The threshold was
chosen with protein sequences of average length in mind. Consequently,
many positions in very long sequences may match motifs with scores above
this threshold by chance, making the results difficult to interpret.
Selecting this option causes the motif display threshold to take
sequence length into account. This will reduce the number of weak motifs
displayed in long sequences and minimize the size of the output file.
MAST can automatically generate the reverse complement strand for each
nucleotide sequence in the database and treat it in three different ways.
("Given strand" refers to the sequence as it appears in the database MAST
is searching.):
combine with given strand
MAST searches for motif occurrences on either the given strand or
its reverse complement together, not allowing occurrences on the two
strands to overlap each other, and displays them together as a single
sequence. This allows motifs to occur on either strand and still count
toward the overall E-value of the match. (The given strand is the
sequence as it appears in the database MAST is searching.)
treat as separate sequence
MAST to search for motifs in both the given strand and its reverse
complement, treating them as two, independent sequences. As of version
4.3.2 the results are displayed together in the html though in previous
versions the results were displayed separately for the two strands, as
though both had occurred in the database.
none
MAST searches only the given strand of each sequence in the database.
Note: this field has no effect when the database contains protein sequences.
Click on the menu at the left to see which of the following motif input methods are available.
Type in motifs
When this option is available you may directly input multiple motifs
by typing them (or using "cut-and-paste").
First select the desired motif alphabet using the menu
immediately to the left. If you select the "Custom" option then
you must provide an alphabet definition
in the file input that immediately follows. Warning: custom alphabets are case-sensitive.
You may optionally give each motif an identifier and alternate name by
inputting a line like >Identifer Alternate-Name preceeding the motif.
You can then enter each motif as either matrices, sequence sites or regular expressions.
You can enter multiple motifs by typing an empty line after each motif.
Individual motifs will be shown in square brackets, and errors in your
motifs will be highlighted in red while warnings will be highlighted in
yellow.
Mouse-over individual motifs to display their sequence logos.
View the examples for more information on what is possible.
Upload motifs
When this option is available you may upload a file containing
motifs in MEME motif format. This includes the outputs generated by MEME
and DREME, as well as files you create using the
motif conversion scripts
or manually following the
MEME motif format guidelines.
Databases (select category)
When this option is available you can select the category of
motif database desired from the list below it. Then select the motif
database from the displayed list.
Consult the
motif database documentation
for descriptions of all the motif databases present on this MEME Suite server.
Submitted motifs
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.
By selecting this option you will input the motifs sent by that program.
You may input both probability and count matrices of either orientation
and the rules described below will be used to convert the matrix into a
MEME formatted motif.
Alphabet Order
The counts/probabilities are expected to be ordered based on the
alphabetical ordering of their codes. So DNA is ordered ACGT and
protein is ordered ACDEFGHIKLMNPQRSTVWY. For custom alphabets the ordering
goes uppercase letters (A-Z), lowercase letters (a-z), numbers (0-9) and
finally the symbols '*', '-' and '.'.
Matrix Orientation
Matrix motifs may be input with either one position per row (preferred)
which is called row orientation, or one position per column which is
called column orientation. The orientation is determined by picking
which dimension (row or column) is equal to the alphabet size. If both
dimensions are equal to the alphabet size then row orientation is assumed.
If neither dimension is equal to the alphabet size then the closest
that is still smaller than the alphabet size is picked, however if both
are equally smaller then column orientation is assumed. Finally if none of
the above rules work to determine the orientation then row orientation is
assumed.
Site counts
Once the orientation is determined, the sum of the numbers that make up
the first position is calculated and rounded to the nearest integer.
If that value is larger than 1 then the matrix is assumed to be a count
matrix and that value is used as the site count, otherwise the matrix is
assumed to be a probability matrix and a site count of 20 is used.
Converting to a normalized probability matrix
Once the orientation is determined then each number in the matrix is
converted to a normalized probability by dividing by the sum of all the
numbers for that motif position. If any numbers are missing they are
assumed to have the value zero. As a special case if all numbers in a
motif position have the value zero then they are given the uniform
probability of 1 / alphabet size.
Yellow highlighting and red annotations
Red asterisks (*) indicate where the
parser thinks values are missing. A yellow highlighted row or column
with a red number at the end indicates that the counts for that position
don't sum to the same count as the first position. The red number shows
the difference. If the red number is negative then that position sums to
less then the first position, if it is positive then it sums to more than
the first position.
Typed Motifs - Sequence Sites or Regular Expressions
You may input one or more sites of the motif including using ambiguity
codes or bracket expressions to represent multiple possibilities for a
single motif position.
Ambiguity Codes
The DNA and protein alphabets include additional codes that represent
multiple possible bases. For example the DNA alphabet includes W (for weak)
which represents that the given position could be either a A (for adenosine)
or a T (for thymidine).
Bracket Expressions
Bracket expressions also group together multiple codes so they share
a single position. Their syntax is a opening square bracket '[' followed
by one or more codes and a closing square bracket ']'. For example with a
DNA motif the bracket expression [AT] means that both A and T are
acceptable and is equivalent to the ambiguity code W. Any repeats of a
base in a bracket expression are ignored so for example a DNA bracket
expression [AAT] has the same effect as [AT] or [AW] or W.
Multiple sites
When only one site is provided the site count is set to 20, however
you can precisely control the motif by providing multiple sites. Each of
these sites can still contain ambiguity codes and bracket expressions
but a single count will be divided among the selected bases for each
position. When multiple sites are provided the site count will be set
to the number of sites provided.
DNA motifs support the standard 4 codes for the bases: adenosine (A),
cytidine (C), guanosine (G) and thymidine (T) as well as supporting
the following ambiguity codes.
When enabled this field supports selecting motifs from the file with a
space separated list of motif identifiers and/or their positions in the
file.
Any numbers in the range 1 to 999 are assumed to refer to the position
of the selected motif in the file, so the entry "3" always refers to the
third motif. Any other entry is assumed to be a motif identifier.
Motif identifiers can not start with a dash and can only contain
alphanumeric characters as well as colon ':', underscore '_', dot '.'
and dash '-'.
This option can help change the alphabet of motifs from
a base alphabet to a derived alphabet.
This might be useful if you need to compare an extended DNA motif with
a library of DNA motifs, or if you wish to compare RNA motifs to DNA motifs.
Note that this option will also let you do nonsensical things like compare
Protein motifs to DNA motifs so use it with care.
The derived alphabet must have all the core symbols of the alphabet
that it is derived from. For example if the alphabet is derived from DNA
it must have ACGT as core symbols. Expanding the alphabet adds frequencies
of zero for every symbol in the derived alphabet that did not exist in the
base alphabet.
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
FASTA format.
Upload sequences
When this option is available you may upload a file containing
sequences in FASTA format.
Upload BED file
When this option is available you may upload a file containing
sequence coordinates in BED format.
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 HERE.
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.
By selecting this option you will input the sequences sent by that program.
Specify a file to upload containing
sequence coordinates in BED format.
The file must be based on the exact genome version you specified in the
menus above.
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 position specific prior that
has been created by the MEME Suite create-priors
utility. You can see a description of the sequence databases
for which we provide tissue/cell-specific priors
here.
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!
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.
