diff GEMBASSY-1.0.3/doc/text/gwvalue.txt @ 2:8947fca5f715 draft default tip

Uploaded

--- a/GEMBASSY-1.0.3/doc/text/gwvalue.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-                                    gwvalue
-Function
-
-   Calculate the 'relative adaptiveness of each codon' (W)
-
-Description
-
-   gwvalue calculates the 'relative adaptiveness of each codon' (W value)
-   which is essential in CAI analysis. W value is calculated by setting the
-   best codon to 1 and calculating the proportion of the other codons.
-    
-   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 gwvalue
-
-% gwvalue refseqn:NC_000913
-Calculate the 'relative adaptiveness of each codon' (W)
-Codon usage output file [nc_000913.gwvalue]: 
-
-   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    [*.gwvalue] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -include            string     [ribosomal.*protein] Regular expression to
-                                  include genes in a reference set a reference
-                                  set in several studies are in-built 1:
-                                  Nakamura and Tabata, 2: Sharp and Li, 3:
-                                  Sakai et al. (Any string)
-   -exclude            string     [[Mm]itochondrial] Regular expression to
-                                  exclude genes from a reference set (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
-
-   gwvalue reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gwvalue is to a plain text file.
-
-   File: nc_000913.gwvalue
-
-Sequence: NC_000913
-Reference set of highly expressed genes
-product
-30S ribosomal subunit protein S20
-30S ribosomal subunit protein S2
-ribosomal protein S12 methylthiotransferase; radical SAM superfamily
-ribosomal protein S6 modification protein
-30S ribosomal subunit protein S1
-ribosomal-protein-S5-alanine N-acetyltransferase
-50S ribosomal subunit protein L32
-
-   [Part of this file has been deleted for brevity]
-
-T,acc,1.0000
-T,acg,0.2234
-T,act,0.9734
-V,gta,0.4960
-V,gtc,0.2281
-V,gtg,0.3422
-V,gtt,1.0000
-W,tgg,1.0000
-Y,tac,1.0000
-Y,tat,0.5310
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Sharp PM et al. (2005) Variation in the strength of selected codon usage
-      bias among bacteria, Nucleic Acids Res. 33(4):1141-1153
-
-   Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
-      conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.
-
-   Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
-      codon usage trends in seven microbial genomes, Microb.Comp.Genomics
-      2:299-312.
-
-   Sharp and Li (1987) The codon Adaptation Index--a measure of directional
-      synonymous codon usage bias, and its potential applications, Nucleic
-      Acids Res. 15:1281-1295.
-
-   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
-
-   genc Calculate the effective number of codons (Nc)
-   gew  Calculate a measure of synonymous codon usage evenness (Ew)
-   gfop Calculate the frequency of optimal codons (Fop)
-   gscs Calculates the scaled chi-square
-
-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.
-