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

Initial upload

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                                      gbui
Function

   Calculates base usage indices for protein-coding sequences

Description

   gbui calculates base usage indices of protein-coding sequences (excluding
   start and stop codons) for each gene. Indices calculated are as follows,
      acgt: Total bumber of bases (A+T+G+C)
      ryr:  Purine/Pyrimidine ratio (A+G)/(T+C)
      gcc:  G+C content (G+C)/(A+T+G+C)
      Hgc:  entropy of G+C content (G+C)/(A+T+G+C)
      gcs:  GC skew (C-G)/(C+G)
      ats:  AT skew (A-T)/(A+T)
    
   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 gbui

% gbui refseqn:NC_000913
Calculates base usage indices for protein-coding sequences
Program compseq output file [nc_000913.gbui]: 

   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    [*.gbui] Program compseq output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include when translating using standard
                                  codon table
   -position           menu       [all] Codon position (Values: all (Assess
                                  overall base usage of the gene); 1 (Assess
                                  base usage at 1st position of codons); 2
                                  (Assess base usage at 2nd position of
                                  codons); 3 (Assess base usage at 3rd
                                  position of codons))
   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
                                  expression to delete key (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

   gbui reads one or more nucleotide sequences.

Output file format

   The output from gbui is to a plain text file.

   File: nc_000913.gbui

Sequence: NC_000913
acgt,ryr,gcc,Hgc,gcs,ats,gene
60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL
2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA
927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB
1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC
291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX
771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA
1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ
948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB

   [Part of this file has been deleted for brevity]

507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX
642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC
864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob
468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA
684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB
1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC
1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD
711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA
135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY
681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD


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

   gdinuc Calculates dinucleotide 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.