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

Initial upload

0:8300eb051bea

                                      gphx
Function

   Identify predicted highly expressed gene

Description

   gphx calculates codon usage differences between gene classes for identifying
   Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is
   identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's
   nature. PHX genes are known to generally have favorable codon usage, strong
   SD sequences, and probably stronger conservation of promoter sequences.
   A gene is idenfitied as PA if BgC and BgH is greater than the median of
   BgC for every gene with a length close to the gene.

   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 gphx

% gphx refseqn:NC_000913
Identify predicted highly expressed gene
Codon usage output file [nc_000913.gphx]: 

   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    [*.gphx] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include when translating using standard
                                  codon table
   -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

   gphx reads one or more nucleotide sequences.

Output file format

   The output from gphx is to a plain text file.

   File: nc_000913.gphx

Sequence: NC_000913
BgC,BgH,E_g,phx,pa,gene
0.8070,0.8977,0.8990,0,1,thrL
0.1857,0.5958,0.3116,0,0,thrA
0.2323,0.5964,0.3896,0,0,thrB
0.2353,0.6064,0.3881,0,0,thrC
0.4353,0.6020,0.7231,0,1,yaaX
0.2961,0.6790,0.4361,0,0,yaaA
0.2233,0.7009,0.3186,0,0,yaaJ
0.4149,0.3071,1.3511,1,0,talB

   [Part of this file has been deleted for brevity]

0.3255,0.7038,0.4625,0,0,yjjX
0.3531,0.5906,0.5979,0,0,ytjC
0.2257,0.5235,0.4311,0,0,rob
0.3584,0.6809,0.5264,0,0,creA
0.3455,0.7950,0.4346,0,0,creB
0.2298,0.7154,0.3212,0,0,creC
0.3299,0.7916,0.4167,0,0,creD
0.3543,0.3786,0.9357,0,0,arcA
0.7295,0.8286,0.8804,0,1,yjjY
0.4028,0.8401,0.4795,0,0,yjtD


Data files

   None.

Notes

   None.

References

   CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm

   Henry I., Sharp PM. (2007) Predicting gene expression level from codon
      usage bias Mol Biol Evol, 24(1):10-2.

   Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse
      prokaryotic genomes J.Bacteriol, 182(18):5238-5250.

   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

   gcai Calculate codon adaptation index for each gene
   gp2  Calculate the P2 index of each gene

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.