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 nameDescription
msbarMutate 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.

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