| ## EMBOSS: shuffleseq

# Program shuffleseq

## Function

Shuffles a set of sequences maintaining composition

## Description

This takes a sequence as input and outputs one or more sequences whose order has been randomly shuffled. No bases or residues are changed, only their order.

The number of shuffled sequences output can be set by the '-shuffle' qualifier.

## Usage

Here is a sample session with shuffleseq making two randomised copies of the input sequence.

    % shuffleseq -shuffle 2
    Shuffles a set of sequences maintaining composition
    Input sequence(s): embl:mmam
    Output sequence [mmam.fasta]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers: (none)
       Advanced qualifiers:
       -shuffle            integer    Number of shuffles

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-shuffle | Number of shuffles | Any integer value | 1

## Input file format

The USA of one or more sequences.

## Output file format

The output is a sequence (by default in FASTA format) with the same base composition as the input.

Each run will produce a different sequence. Here is the output from the example above:

    >MMAM L48662 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody
    heavy chain mRNA.
    ggcggcctccggtcaccaacctaattcggtgtcagtggcggccaagcatcctttatcaca
    agtcgacccattttcttcgtaccacacaatagctctaacgttcttgtgatagtttaggag
    ttgcagagcttcgagaggtacactaacaaggaaagagtgcgacaggaaccaaggagcatg
    aaatgaaacagctcctaaatctccaacgctaagactcggccattgctagtattantataa
    attcattcacagcccgttagcggccttttaatcacctgaaggcccccatatattaggcgt
    gacaggtatccaggcggacctttcgttcgtggtaagggtcgaatggagtgctacagtatn
    ctgaac
    >MMAM L48662 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody
    heavy chain mRNA.
    ccaaaacaatcctagatgaacctctgccgattcaaggcagntagctttctgtaagctcgt
    ttgagatgctaatgtagccggtgaatagaagcctaggactcgcttcccactttctgcttt
    aagattatcgagccctacggaatgagctggaatctggtcttaggcattacgaacagnacg
    ggtggacgggggaccaaaagtggaggggatttctccctgctgacaaaagacactatagta
    tccccctggcattctagccgtcccgtctcgtgctagtaacggtcacagcaatgggagtct
    tgtagaacaataacggccgtctatgataccaagtcactttagacgtacaatcaaatctca
    tcaacc

Note that these two sequences have the same name.

## Data files

None.

## Notes

This program may be useful for producing sets of sequences which can be used to check the statistics of sequence similarity finding software.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
msbar | Mutate sequence beyond all recognition

## Author(s)

This application was written by Michael Schmitz (mschmitz@lbl.gov)

## History

Finished.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments