The MEME Suite

Various MEME Suite programs require as input a file containing sequences of protein, DNA, RNA or potentially some other custom alphabet. These input files must be in FASTA format which must be plain text, not WORD, .doc, .docx, .rtf or any other word-processor format.

Each FASTA entry consists of a sequence identifier line followed by one or more sequence lines. The sequence identifier line begins with the ">" character in column 1, which must be immediately followed by a sequence identifier (ID). The ID may be followed by an (optional) sequence description (COMMENT). There may be no whitespace between the ">" and the ID, and whitespace must separate the end of the ID from the COMMENT. The format looks like this:

>ID1 COMMENT
SEQUENCE
SEQUENCE
...
>ID2 COMMENT
SEQUENCE
...
      

Some rules about the sequence lines that follow the sequence identifier line:

• For the built-in alphabets like DNA, RNA and protein case doesn't matter.
• White space (spaces and newlines) within the sequence are ignored.
• Characters should be from the alphabet in use which may be a built-in standard or be custom defined.
• The end of a FASTA entry is indicated by the next sequence identifier line (starting with the ">" character in column 1), or by the end of the file.

Here is an example of three protein sequences in FASTA format:

>ICYA_MANSE 
GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY
DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN
LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH

>LACB_BOVIN 
MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA
QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI
DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
KFDKALKALPMHIRLSFNPTQLEEQCHI

>BBP_PIEBR 
NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE
GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN
VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
GSPVVDSQKLVYSDFSEAACKVN
      

When running MEME sequence weights may be specified in the dataset file by special header lines where the unique name is "WEIGHTS" (all caps) and the descriptive text is a list of sequence weights.

Sequence weights are numbers in the range 0 < w ≤ 1. All weights are assigned in order to the sequences in the file. If there are more sequences than weights, the remainder are given weight one. Weights may be specified by more than one "WEIGHTS" entry which may appear anywhere in the file. When weights are used, sequences will contribute to motifs in proportion to their weights.

Here is an example for a file of three sequences where the first two sequences are very similar and it is desired to down-weight them:

>WEIGHTS 0.5 .5 1.0 
>seq1
GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAK
>seq2
GDMFCPGYCPDVKPVGDFDLSAFAGAWHELAK
>seq3
QKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKW