
                             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
