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

Initial upload

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+++ b/GEMBASSY-1.0.3/doc/text/gphx.txt	Fri Jun 26 05:19:29 2015 -0400
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+                                      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.
+