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                                 gcodoncompiler
Function

   Calculate various kinds of amino acid and codon usage data

Description

   gcodoncompiler calculates various kinds of amino acid and codon usage data.
   The following values are calculable:
      A0: Absolute amino acid frequency
      A1: Relative amino acid frequency
      C0: Absolute codon frequency
      C1: Relative codon frequency in a complete sequence
      C2: Relative codon frequency in each amino acid
      C3: Relative synonymous codon usage
      C4: Relative adaptiveness
      C5: Maximum or minor codon

   For amino acids unpresent in a gene, C2-C3 does not calculate the values.
   By using R* in place, such values are hypothesized that alternative
   synonymous codons are used with equal frequency.
    
   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 gcodoncompiler

% gcodoncompiler refseqn:NC_000913
Calculate various kinds of amino acid and codon usage data
Codon usage output file [nc_000913.gcodoncompiler]: 

   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    [*.gcodoncompiler] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include to translate using standard
                                  codon table
   -startcodon         boolean    [N] Include to include start codon
   -stopcodon          boolean    [N] Include to include stop codon
   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
                                  expression to delete key (i.e. amino acids
                                  and nucleotides) (Any string)
   -data               menu       [R0] Kinds of codon usage data. R*
                                  hypothesizes amino acids which are not
                                  present in the gene (Values: A0 (Absolute
                                  amino acid frequency ('AA')); A1 (Relative
                                  amino acid frequency ('RAAU')); C0 (Absolute
                                  codon frequency ('AF')); C1 (Relative codon
                                  frequency in a complete sequence); C2
                                  (Relative codon frequency in each amino acid
                                  ('RF')); C3 (Relative synonymous codon
                                  usage ('RSCU')); C4 (Relative adaptiveness);
                                  i.e., ratio to maximum of minor codon ('W')
                                  C5 (Maximum (1) or minor (0) codon); R0
                                  (Absolute codon frequency ('AF')); R1
                                  (Relative codon frequency in a complete
                                  sequence); R2 (Relative codon frequency in
                                  each amino acid ('RF')); R3 (Relative
                                  synonymous codon usage ('RSCU')); R4
                                  (Relative adaptiveness); i.e., ratio to
                                  maximum of minor codon ('W') R5 (Maximum (1)
                                  or minor (0) codon))
   -[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

   gcodoncompiler reads one or more nucleotide sequences.

Output file format

   The output from gcodoncompiler is to a plain text file.

   File: nc_000913.gcodoncompiler

Sequence: NC_000913
Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag
26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,


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

   gaminoinfo Prints out basic amino acid sequence statistics
   gaaui      Calculates various indece of amino acid usage

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.