gsvalue
Function

   Calculate the strength of selected codon usage bias (S)

Description

   gsvalue calculates the strength of selected codon usage bias (S), also
   known as Sharp's S index. Using four codon pairs that are recognized by the
   same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and
   UAU), and Asn(AAC and AAU), since the former in each of the pairs has
   stronger Watson-Crick pairing, selection towards the former codon can be
   observed for highly expressed genes. S index is therefore the weighted
   average of such bias, giving an over-all value for a genome, indicating its
   strength of selected codon usage bias. See Sharp et al. (2005) for details.
   Sharp originally defined 40 genes as the highly expressed gene group, with
   tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton
   of these genes is not convenient for computational automation, by default,
   this method uses ribosomal proteins as the highly expressed gene group,
   as used by Viera-silva and Rocha (2010).
   However, Sharp's gene group can be optionally used with -sharp option.
   With this option, all of the 40 genes must be named accordingly in the given
   genome file.
    
   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 gsvalue

% gsvalue refseqn:NC_000913
Calculate the strength of selected codon usage bias (S)
Codon usage output file [nc_000913.gsvalue]: 

   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    [*.gsvalue] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sharp              boolean    [N] Include to use the 40 genes used by
                                  Sharp instead of ribosomal proteins
   -[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

   gsvalue reads one or more nucleotide sequences.

Output file format

   The output from gsvalue is to a plain text file.

   File: nc_000913.gsvalue

Sequence: NC_000913 S-value: 1.23467100598485


Data files

   None.

Notes

   None.

References

   Sharp PM et al. (2005) "Variation in the strength of selected codon usage
      bias among bacteria", Nucleic Acids Research, 33(4):1141-1153

   Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
      uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808

   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

   gcbi       Calculates the codon bias index (CBI)
   gdelta_enc Calculate the codon usage bias related to translation optimization              (delta ENC)
   gicdi      Calculates the intrinsic codon deviation index (ICDI)

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.