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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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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 (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 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.