gdeltagcskew
Function

   Calculate strand bias of bacterial genome using delta GC skew index

Description

   gdeltagcskew calculates strand bias of bacterial genome using delta GC skew
   index, first proposed by Rocha et al. (2001), and further extended in 2006.
   Basic idea of delta GC skew index is to calculate the difference of GC skew
   in coding regions residing in leading and lagging strands. Rocha et al.
   (2001) calculates delta GC skew index using the third codon position of
   genes, and Rocha et al. (2006)  modified to only use >fourfold degenerate
   codons.
    
   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 gdeltagcskew

% gdeltagcskew refseqn:NC_000913
Calculate strand bias of bacterial genome using delta GC skew index
Program compseq output file [nc_000913.gdeltagcskew]: 

   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)
  [-outfile]           outfile    [*.gdeltagcskew] Program compseq output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -at                 boolean    [N] Include when observing AT skew instead
                                  of GC skew
   -purine             boolean    [N] Include when observing purine (AG/TC)
                                  skew
   -keto               boolean    [N] Include when observing keto (TG/AC) skew
   -method             selection  [degenerate] Choose the nucleotides to use
                                  'degenerate', 'gc3', or 'all'
   -[no]accid          boolean    [Y] Include to use sequence accession ID as
                                  query

   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

   "-outfile" associated qualifiers
   -odirectory2        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

   gdeltagcskew reads one or more nucleotide sequences.

Output file format

   The output from gdeltagcskew is to a plain text file.

   File: nc_000913.gdeltagcskew

Sequence: NC_000913 DELTA-GCskew -0.108937


Data files

   None.

Notes

   None.

References

   Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
      Genomes, Molecular Biology and Evolution, 18(9):1789-1799

   Rocha EPC et al. (2006) Similar compositional biases are caused by very
      different mutational effects, Genome Research, 16:1537-1547

   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

   gb1      Calculate strand bias of bacterial genome using B1 index
   gb2      Calculate strand bias of bacterial genome using B2 index
   ggcsi    GC Skew Index: an index for strand-specefic mutational bias
   gldabias Calculate strand bias of bacterial genome using linear
            discriminant analysis (LDA)

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.