annotate GEMBASSY-1.0.3/doc/text/gkmertable.txt @ 0:8300eb051bea draft

Initial upload

                                   gkmertable
Function

   Create an image showing all k-mer abundance within a sequence

Description

   gkmertable creates an image showing the abundance of all k-mers
   (oligonucleotides of length k) in a given sequence. For example, for
   tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each
   representing an oligomer. Oligomer name and abundance is written within
   these boxes, and abundance is also visualized with the box color, from
   white (none) to black (highly frequent).

   This k-mer table is alternatively known as the FCGR (frequency matrices
   extracted from Chaos Game Representation).
   Position of the oligomers can be recursively located as follows:
   For each letter in an oligomer, a box is subdivided into four quadrants, 
   where A is upper left, T is lower right, G is upper right, and C is lower
   left.

   Therefore, oligomer ATGC is in the 
   A = upper left quadrant
   T = lower right within the above quadrant
   G = upper right within the above quadrant
   C = lower left within the above quadrant
   More detailed documentation is available at 
   http://www.g-language.org/wiki/cgr
    
   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 gkmertable

% gkmertable refseqn:NC_000913
Create an image showing all k-mer abundance within a sequence
Created gkmertable.1.png

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -format             string     [png] Output file format. Dependent on
                                  'convert' command (Any string)
   -k                  integer    [6] Length of oligomer (Any integer value)
   -goutfile           string     [gkmertable] Output file for non interactive
                                  displays (Any string)

   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

   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

   gkmertable reads one or more nucleotide sequences.

Output file format

   The output from gkmertable is to an image file.

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

   gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
   goligomercounter       Counts the number of given oligomers in a sequence
   goligomersearch        Searches oligomers in given sequence
   gsignature             Calculate oligonucleotide usage (genomic signature)

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.