diff GEMBASSY-1.0.3/doc/text/gshuffleseq.txt @ 2:8947fca5f715 draft default tip

Uploaded

--- a/GEMBASSY-1.0.3/doc/text/gshuffleseq.txt	Fri Jun 26 05:20:29 2015 -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 ([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.
-