diff GEMBASSY-1.0.3/doc/text/ggeneskew.txt @ 0:8300eb051bea draft

Initial upload

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+++ b/GEMBASSY-1.0.3/doc/text/ggeneskew.txt	Fri Jun 26 05:19:29 2015 -0400
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+                                   ggeneskew
+Function
+
+   Calculate the gene strand bias of the given genome
+
+Description
+
+   ggeneskew calculates and plots the strand bias of genes (or the GC skew
+   within them). By default, this program visualizes the gene strand preference
+   (1 for direct, -1 for complement strand), but by specifying -base option
+   option, GC/AT/Purine/Keto skews of the coding regions or more specifically
+   in the GC3 (third codon position) with -gctri option can be calculated.
+    
+   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 ggeneskew
+
+% ggeneskew refseqn:NC_000913
+Calculate the gene strand bias of the given genome
+Program compseq output file (optional) [nc_000913.ggeneskew]: 
+
+   Go to the input files for this example
+   Go to the output files for this example
+
+   Example 2
+
+% ggeneskew refseqn:NC_000913 -plot -graph png
+Calculate the gene strand bias of the given genome
+Created ggeneskew.1.png
+
+   Go to the input files for this example
+   Go to the output files for this example
+
+Command line arguments
+
+   Standard (Mandatory) qualifiers (* if not always prompted):
+  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
+                                  format, or reference (input USA)
+*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
+                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
+                                  tek, tekt, none, data, xterm, png, gif, svg)
+*  -outfile            outfile    [*.ggeneskew] Program compseq output file
+                                  (optional)
+
+   Additional (Optional) qualifiers: (none)
+   Advanced (Unprompted) qualifiers:
+   -window             integer    [10000] Window size to observe (Any integer
+                                  value)
+   -slide              integer    [10000] Window slide size (Any integer
+                                  value)
+   -cumulative         boolean    [N] Input 1 to calculate cumulative skew
+   -base               selection  [none] Input 'gc', 'at', 'purine', or 'keto'
+                                  for observing GC/AT/Purine/Keto skews
+   -gctri              boolean    [N] Include to use only the third codon
+                                  positions
+   -[no]accid          boolean    [Y] Include to use sequence accession ID as
+                                  query
+   -plot               toggle     [N] Include to plot result
+
+   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
+
+   "-graph" associated qualifiers
+   -gprompt            boolean    Graph prompting
+   -gdesc              string     Graph description
+   -gtitle             string     Graph title
+   -gsubtitle          string     Graph subtitle
+   -gxtitle            string     Graph x axis title
+   -gytitle            string     Graph y axis title
+   -goutfile           string     Output file for non interactive displays
+   -gdirectory         string     Output directory
+
+   "-outfile" associated qualifiers
+   -odirectory         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
+
+   ggeneskew reads one or more nucleotide sequences.
+
+Output file format
+
+   The output from ggeneskew is to a plain text file or the EMBOSS graphics
+   device.
+
+   File: nc_000913.ggeneskew
+
+Sequence: NC_000913
+location,gene None skew
+190,0.294118
+337,-0.058914
+2801,-0.120000
+3734,-0.070588
+5234,0.037500
+5683,0.020725
+6529,0.032765
+8238,-0.028226
+
+   [Part of this file has been deleted for brevity]
+
+4631820,-0.093407
+4632464,-0.006479
+4633544,-0.120690
+4634030,-0.060367
+4634719,-0.104167
+4636201,-0.144560
+4637613,0.010929
+4638425,0.200000
+4638965,-0.081871
+,
+
+
+Data files
+
+   None.
+
+Notes
+
+   None.
+
+References
+
+   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
+
+   ggcskew      Calculates the GC skew of the input sequence
+   ggcwin       Calculates the GC content along the given genome
+   ggenomicskew Calculates the GC skew in different regions of the given genom
+
+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.
+