comparison GEMBASSY-1.0.3/doc/text/gwvalue.txt @ 0:8300eb051bea draft

Initial upload

0:8300eb051bea

                                    gwvalue
Function

   Calculate the 'relative adaptiveness of each codon' (W)

Description

   gwvalue calculates the 'relative adaptiveness of each codon' (W value)
   which is essential in CAI analysis. W value is calculated by setting the
   best codon to 1 and calculating the proportion of the other 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 gwvalue

% gwvalue refseqn:NC_000913
Calculate the 'relative adaptiveness of each codon' (W)
Codon usage output file [nc_000913.gwvalue]: 

   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    [*.gwvalue] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -include            string     [ribosomal.*protein] Regular expression to
                                  include genes in a reference set a reference
                                  set in several studies are in-built 1:
                                  Nakamura and Tabata, 2: Sharp and Li, 3:
                                  Sakai et al. (Any string)
   -exclude            string     [[Mm]itochondrial] Regular expression to
                                  exclude genes from a reference set (Any
                                  string)
   -[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

   gwvalue reads one or more nucleotide sequences.

Output file format

   The output from gwvalue is to a plain text file.

   File: nc_000913.gwvalue

Sequence: NC_000913
Reference set of highly expressed genes
product
30S ribosomal subunit protein S20
30S ribosomal subunit protein S2
ribosomal protein S12 methylthiotransferase; radical SAM superfamily
ribosomal protein S6 modification protein
30S ribosomal subunit protein S1
ribosomal-protein-S5-alanine N-acetyltransferase
50S ribosomal subunit protein L32

   [Part of this file has been deleted for brevity]

T,acc,1.0000
T,acg,0.2234
T,act,0.9734
V,gta,0.4960
V,gtc,0.2281
V,gtg,0.3422
V,gtt,1.0000
W,tgg,1.0000
Y,tac,1.0000
Y,tat,0.5310


Data files

   None.

Notes

   None.

References

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

   Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
      conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.

   Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
      codon usage trends in seven microbial genomes, Microb.Comp.Genomics
      2:299-312.

   Sharp and Li (1987) The codon Adaptation Index--a measure of directional
      synonymous codon usage bias, and its potential applications, Nucleic
      Acids Res. 15:1281-1295.

   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

   genc Calculate the effective number of codons (Nc)
   gew  Calculate a measure of synonymous codon usage evenness (Ew)
   gfop Calculate the frequency of optimal codons (Fop)
   gscs Calculates the scaled chi-square

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.