
                                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
   
   This makes two randomised copies of the input sequence:
   

% shuffleseq -shuffle 2 
Shuffles a set of sequences maintaining composition
Input sequence(s): tembl:mmam
Output sequence [mmam.fasta]: 
   
   Go to the input files for this example
   Go to the output files for this example
   
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                boolean    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

   shuffleseq reads one or more sequence USAs.
   
  Input files for usage example
  
   'tembl:mmam' is a sequence entry in the example nucleic acid database
   'tembl'
   
  Database entry: tembl:mmam
  
ID   MMAM       standard; RNA; MUS; 366 BP.
XX
AC   L48662;
XX
SV   L48662.1
XX
DT   04-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 4)
XX
DE   Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy
DE   chain mRNA.
XX
KW   .
XX
OS   Mus musculus (house mouse)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-366
RX   MEDLINE; 96409289.
RX   PUBMED; 8814271.
RA   Wloch M.K., Alexander A.L., Pippen A.M., Pisetsky D.S., Gilkeson G.S.;
RT   "Differences in V kappa gene utilization and VH CDR3 sequence among
RT   anti-DNA from C3H-lpr mice and lupus mice with nephritis";
RL   Eur. J. Immunol. 26(9):2225-2233(1996).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..366
FT                   /db_xref="taxon:10090"
FT                   /organism="Mus musculus"
FT                   /strain="C3H/HeJ-lpr/lpr"
FT                   /cell_line="C3H/F2-11"
FT                   /cell_type="hybridoma"
FT                   /tissue_type="spleen"
XX
SQ   Sequence 366 BP; 100 A; 90 C; 85 G; 89 T; 2 other;
     gagnnccagc tgcagcagtc tggacctgag ctggtaaagc ctggggcttc agtgaagatg        6
0
     tcctgcaagg cttctggata cacattcact agctatgtta tgcactgggt gaatcagaag       12
0
     cctgggcagg gccttgagtg gattggatat attaatcctt acaatgatgg tactaactac       18
0
     aatgagaagt tcaaaggcaa ggccacactg acttcagaca aatcctccag cacagcctac       24
0
     atggagttca gcagcctgac ctctgaggac tctgcggtct attactgtgc aagaaaaact       30
0
     tcctactata gtaacctata ttactttgac tactggggcc aaggcaccac tctcacagtc       36
0
     tcctca                                                                  36
6
//
   
Output file format

  Output files for usage example
  
  File: mmam.fasta
  
>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibo
dy heavy chain mRNA.
caatccaaacgcagtggttgccgagcccggaagaaccctctagggttattacttacagct
gacactggggtagagcggtccagcagtgttagtcttgcagtgtctgtctatcggacaagc
ggtcataggaactcagcagatccctcctggatcgacacaccaacgagtagattcgatcta
gctgttagcgacctaatatcaacttcactaccgccgaaccaataagctaccggctttaac
acgcgatatttcccatagatccaataaacaatttcatgtggtttggggaaaaaaactttg
ccagtaatttggcngtgacgccatcccaatggngagtgcataaaatgtggtggcgcgcat
tatttc
>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibo
dy heavy chain mRNA.
tgttctctagaaaatcacgacatttgtggtgtaccaggccctcgcggaaacgcggtaaaa
aaacgataactggccaggcgagaacataaggcaatctagagagcgacaganggggaaccg
agttgtgcgccagtttatctatcgggcggtcgcgcccgcttcctccccaaaacttaacgg
agctgcacattaacgtggctgacgatactatttacccagatagccttggttccttagatt
cgaagttgcactgttgtagacgagtggaaataaagtccgcatattacttaaatccgngtc
actggatgctatctatgtattctactacactagctggctcacacatagataactccctta
ccggct
   
   Each run will produce a different sequence.
   
   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
