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        60
     tcctgcaagg cttctggata cacattcact agctatgtta tgcactgggt gaatcagaag       120
     cctgggcagg gccttgagtg gattggatat attaatcctt acaatgatgg tactaactac       180
     aatgagaagt tcaaaggcaa ggccacactg acttcagaca aatcctccag cacagcctac       240
     atggagttca gcagcctgac ctctgaggac tctgcggtct attactgtgc aagaaaaact       300
     tcctactata gtaacctata ttactttgac tactggggcc aaggcaccac tctcacagtc       360
     tcctca                                                                  366
//

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 antibody heavy chain mRNA.
caatccaaacgcagtggttgccgagcccggaagaaccctctagggttattacttacagct
gacactggggtagagcggtccagcagtgttagtcttgcagtgtctgtctatcggacaagc
ggtcataggaactcagcagatccctcctggatcgacacaccaacgagtagattcgatcta
gctgttagcgacctaatatcaacttcactaccgccgaaccaataagctaccggctttaac
acgcgatatttcccatagatccaataaacaatttcatgtggtttggggaaaaaaactttg
ccagtaatttggcngtgacgccatcccaatggngagtgcataaaatgtggtggcgcgcat
tatttc
>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody 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 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.

Comments