annotate GEMBASSY-1.0.3/doc/text/gshuffleseq.txt @ 1:84a17b3fad1f draft

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                                  gshuffleseq
Function

   Create randomized sequence with conserved k-mer composition

Description

   gshuffleseq shuffles and randomizes the given sequence, conserving the
   nucleotide/peptide k-mer content of the original sequence.

   For k=1, i.e. shuffling sequencing preserving single nucleotide composition,
   Fisher-Yates Algorithm is employed.
   For k>1, shuffling preserves all k-mers (all k where k=1~k). For example,
   k=3 preserves all triplet, doublet, and single nucleotide composition.
   Algorithm for k-mer preserved shuffling is non-trivial, which is solved
   by graph theoretical approach with Eulerian random walks in the graph of
   k-1-mers. See Jiang et al., Kandel et al., and Propp et al., for details
   of this algorithm.
    
   G-language SOAP service is provided by the
   Institute for Advanced Biosciences, Keio University.
   The original web service is located at the following URL:

   http://www.g-language.org/wiki/soap

   WSDL(RPC/Encoded) file is located at:

   http://soap.g-language.org/g-language.wsdl

   Documentation on G-language Genome Analysis Environment methods are
   provided at the Document Center

   http://ws.g-language.org/gdoc/

Usage

Here is a sample session with gshuffleseq

% gshuffleseq tsw:hbb_human
Create randomized sequence with conserved k-mer composition
output sequence [hbb_human.fasta]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -k                  integer    [1] Sequence k-mer to preserve composition
                                  (Any integer value)

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

   The database definitions for following commands are available at
   http://soap.g-language.org/kbws/embossrc

   gshuffleseq reads one or more nucleotide or protein sequences.

Output file format

   The output from gshuffleseq is to .

   File: hbb_human.fasta

>HBB_HUMAN P68871 Hemoglobin subunit beta (Beta-globin) (Hemoglobin beta chain) (LVV-hemorphin-7)
KGWLDLVAGAAHFVRRLKMLLEVDWAAHEERVGTSNPNNALKNEAADVEVHSPTHVNPTQ
LVLVQVGFGTLHLQGVECPKPKPGGVALKPVAHLLAMKECTLVALGSDFYVDHGSDGEDK
GFKAYVLATSFFAYTNFLHGKVKHVLF


Data files

   None.

Notes

   None.

References

   Fisher R.A. and Yates F. (1938) "Example 12", Statistical Tables, London

   Durstenfeld R. (1964) "Algorithm 235: Random permutation", CACM 7(7):420

   Jiang M., Anderson J., Gillespie J., and Mayne M. (2008) "uShuffle: 
      a useful tool for shuffling biological sequences while preserving the
      k-let counts", BMC Bioinformatics 9:192

   Kandel D., Matias Y., Unver R., and Winker P. (1996) "Shuffling biological 
      sequences", Discrete Applied Mathematics 71(1-3):171-185  

   Propp J.G. and Wilson D.B. (1998) "How to get a perfectly random sample 
      from a generic Markov chain and generate a random spanning tree of a 
      directed graph", Journal of Algorithms 27(2):170-217

   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.

   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
      large-scale analysis of high-throughput omics data, J. Pest Sci.,
      31, 7.

   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
      Analysis Environment with REST and SOAP Web Service Interfaces,
      Nucleic Acids Res., 38, W700-W705.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   shuffleseq Shuffles a set of sequences maintaining composition

Author(s)

   Hidetoshi Itaya ([e-mail])
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

   Kazuharu Arakawa ([e-mail])
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

History

   2012 - Written by Hidetoshi Itaya
   2013 - Fixed by Hidetoshi Itaya

Target users

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

Comments

   None.