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gshuffleseq |
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/
% gshuffleseq tsw:hbb_human Create randomized sequence with conserved k-mer composition output sequence [hbb_human.fasta]: |
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 |
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.
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 |
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
shuffleseq | Shuffles a set of sequences maintaining composition |
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