genc
Function

   Calculate the effective number of codons (Nc)

Description

   genc calculates the effective number of codons (ENC|Nc). ENC is a measure
   for species-independent codon usage bias. Some measures including CAI are
   species-dependent as optimal codons differ. ENC assigns a gene a number
   between 20 to 61 where 20 indicates that one codon is used for each amino
   acid and 61 indicates that each codon is used equally throughout the
   protein sequence.
    
   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 genc

% genc refseqn:NC_000913
Calculate the effective number of codons (Nc)
Codon usage output file [nc_000913.genc]: 

   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    [*.genc] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include when translates using standard
                                  codon table
   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
                                  expression to delete key (i.e. amino acids
                                  and nucleotides) (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

   genc reads one or more nucleotide sequences.

Output file format

   The output from genc is to a plain text file.

   File: nc_000913.genc

Sequence: NC_000913
enc,gene
,thrL
48.41,thrA
54.13,thrB
46.18,thrC
51.65,yaaX
45.71,yaaA
48.54,yaaJ
36.83,talB

   [Part of this file has been deleted for brevity]

51.43,yjjX
46.61,ytjC
49.83,rob
47.74,creA
50.63,creB
51.39,creC
48.42,creD
41.53,arcA
61,yjjY
53.63,yjtD


Data files

   None.

Notes

   None.

References

   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
      usage bias, J Mol Evol, 47(3):268-74.

   Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
      87:23-29.

   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

   gew     Calculate a measure of synonymous codon usage evenness (Ew)
   gfop    Calculate the frequency of optimal codons (Fop)
   gscs    Calculates the scaled chi-square
   gwvalue Calculate the 'relative adaptiveness of each codon' (W)

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.