# The MEME Suite

## Motif-based sequence analysis tools

## fasta-shuffle-letters

### Usage:

`fasta-shuffle-letters [options] <sequence file> [<output file>]`

### Description

The program fasta-shuffle-letters creates a shuffled version of a FASTA file. The letters in each sequence in the input file are shuffled in such a way that k-mer frequencies are exactly preserved where k is by default 1 but may be set by the "-kmer" option.

The underlying implementation uses uShuffle.

### Input

Sequences in FASTA format from a file.

### Output

Writes a FASTA format file to the optional output file or standard output if it is left unspecified.

### Options

Option | Parameter | Description | Default Behaviour
--- | --- | --- | ---
General Options
-kmer | num | Shuffle the sequences so groups of num symbols appear with exactly the same frequencies. Note that in setting this number you must maintain a balance - the larger the number the more realistic the sequence will be however too large and it will not be shuffled at all! A value of 2 is used by MEME-ChIP. For values larger than 1 specifing the alphabet is highly recommended because it allows for the translation of aliases which may be important in some cases like soft-masked sequence. | A value of 1 is used which allows the shuffle to be completely random.
-copies | num | The number of shuffled copies to create for each sequence in the source. | A single shuffled sequence is created for each sequence in the source.
-dna |  | As if the -alph option was specified with the standard DNA alphabet as input. |
-protein |  | As if the -alph option was specified with the standard protein alphabet as input. |
-rna |  | As if the -alph option was specified with the standard RNA alphabet as input. |
-alph | file | The sequences will have their symbols converted to their primary representation in the given alphabet definition. Any unknown symbols will be converted to the alphabet's wildcard. | When no alphabet is specified symbols must match exactly to be considered the same.
-line | num | The sequences will be output with a maximum of num symbols per line. | A line length of 100 is used.
-tag | text | The name of the sequence will have text appended to it. | The name of the sequence will have "_shuf" appended to it.
-seed | num | Set the seed of the random number generator to num. | Seed the random number generator from the computer as randomly as possible.
-help |  | Display a brief help message and exit. |