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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
seqall Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-outseq]
(Parameter 2)
seqout Sequence filename and optional format (output USA) Writeable sequence <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-k integer Sequence k-mer to preserve composition Any integer value 1

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

Program name Description
shuffleseq Shuffles a set of sequences maintaining composition

Author(s)

   Hidetoshi Itaya (celery@g-language.org)
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

  Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
  Institute for Advanced Biosciences, Keio University
  252-0882 Japan

History

2012 - Written by Hidetoshi Itaya

Target users

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

Comments

None.