Motif Input Template

Information about the motif field would be displayed here.

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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.

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#### Typed Motifs - Matrices

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.

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#### 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.

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#### DNA Alphabet

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.

Description | Code | Bases
--- | --- | ---
Uracil | U | T
Weak | W | A, T
Strong | S | C, G
Amino | M | A, C
Keto | K | G, T
Purine | R | A, G
Pyrimidine | Y | C, T
Not A | B | C, G, T
Not C | D | A, G, T
Not G | H | A, C, T
Not T | V | A, C, G
Any | N | A, C, G, T

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#### Protein Alphabet

Protein motifs support the standard 20 codes for the amino acids: Alanine (A), Arginine (R), Asparagine (N), Aspartic acid (D), Cysteine (C), Glutamic acid (E), Glutamine (Q), Glycine (G), Histidine (H), Isoleucine (I), Leucine (L), Lysine (K), Methionine (M), Phenylalanine (F), Proline (P), Serine (S), Threonine (T), Tryptophan (W), Tyrosine (Y) and Valine (V) as well as supporting the following ambiguity codes.

Description | Code | Bases
--- | --- | ---
Asparagine or aspartic acid | B | N, D
Glutamine or glutamic acid | Z | E, Q
Leucine or Isoleucine | J | I, L
Unspecified or unknown amino acid | X | A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y

Note that the two amino acids Selenocysteine (U) and Pyrrolysine (O) are not supported by the MEME Suite.

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#### Typed Motifs - Examples

Single site motif using ambiguity codes N and R or bracket expressions. These give an approximation of the other motifs below.

NTRGGTCAN or [ACGT]T[AG]GGTCA[ACGT]

Multiple site motif. This lists all 28 sites and gives the same result as the count matrix below.

CTAGGTCAT ATAGGTCAC GTAGGTCAC GTAGGGCAC GTAGGGCAC GTGGGTCAC GTAGGTCAC GTAGGTCAC TTGGGTCAC CTAGGTCAT CTAGGTCAT CTAGGTCAT CTGGGTCAC ATAGGTCAG GTAGGTCAA GTAGGTGAG ATGGGTCAC GTAGGTCAG GTGGGTGAA GTAGGGCAC CTGGGTCAC TTGGGTCAC CTAGGTCAC GAAGGTGAC GTAGGTAAA GTAGGTCAA CAGCAGCTG TAGGTCACA

Count matrix motif showing row and column orientations.

3 8 14 3 3 0 0 25 19 0 9 0 0 1 27 0 1 0 26 1 0 1 4 23 2 23 3 0 26 1 0 1 5 15 4 4 or 3 3 19 0 1 0 2 26 5 8 0 0 1 0 1 23 1 15 14 0 9 27 26 4 3 0 4 3 25 0 0 1 23 0 1 4

Note that all of these can be used with an identifier and alternate name like these 3 count matrix motifs from Jaspar.

>MA0001.1 SEP4 0 3 79 40 66 48 65 11 65 0 94 75 4 3 1 2 5 2 3 3 1 0 3 4 1 0 5 3 28 88 2 19 11 50 29 47 22 81 1 6 >MA0002.1 RUNX1 10 12 4 1 2 2 0 0 0 8 13 2 2 7 1 0 8 0 0 1 2 2 3 1 1 0 23 0 26 26 0 0 4 11 11 14 24 1 16 0 0 25 16 7 >MA0003.1 TFAP2A 0 0 0 22 19 55 53 19 9 0 185 185 71 57 44 30 16 78 185 0 0 46 61 67 91 137 79 0 0 0 46 48 19 11 13 19
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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 '-'.

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Select the desired motif database.

Consult the motif database documentation for descriptions of all the DNA and RNA motif databases present on this MEME Suite server.

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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.

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## Input the motifs

#### Enter motifs you wish to scan with.

Only select motif(s):
Allow alphabet expansion