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

Initial upload

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+++ b/GEMBASSY-1.0.3/doc/text/gaaui.txt	Fri Jun 26 05:19:29 2015 -0400
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+                                     gaaui
+Function
+
+   Calculates various indece of amino acid usage
+
+Description
+
+   gaaui calculates amino acid usage indices for proteins (excluding
+   formylmethionine). Calculated indices are as follows,
+      Laa:   Length in amino acids
+      ndaa:  Number of different amino acids
+      Haau:  Entropy of amino acid usage
+      mmw:   Mean molecular weight
+      gravy: Mean hydropathic indices of each amino acid
+      aroma: Relative frequency of aromatic amino acids
+    
+   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 gaaui
+
+% gaaui refseqn:NC_000913
+Calculates various indece of amino acid usage
+AAINDEX entry output file [nc_000913.gaaui]: 
+
+   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    [*.gaaui] AAINDEX entry output file
+
+   Additional (Optional) qualifiers: (none)
+   Advanced (Unprompted) qualifiers:
+   -[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
+
+   gaaui reads one or more nucleotide sequences.
+
+Output file format
+
+   The output from gaaui is to a plain text file.
+
+   File: nc_000913.gaaui
+
+Sequence: NC_000913
+Laa,ndaa,Haau,mmw,gravy,aroma,gene
+20,8,2.4842,117.48,+0.0150,0.0000,thrL
+819,20,4.0887,126.65,+0.0328,0.0659,thrA
+309,20,4.1228,126.35,+0.0181,0.0712,thrB
+427,20,4.0806,128.00,-0.1014,0.0843,thrC
+97,18,3.9165,133.54,-1.0268,0.0928,yaaX
+257,19,4.0733,132.55,-0.4117,0.1089,yaaA
+475,20,4.0413,126.46,+0.6781,0.1242,yaaJ
+316,20,4.0395,128.99,-0.2165,0.0728,talB
+
+   [Part of this file has been deleted for brevity]
+
+169,20,4.0001,124.90,+0.0231,0.0710,yjjX
+214,20,3.9937,129.77,-0.3813,0.0374,ytjC
+288,20,4.1421,132.58,-0.3628,0.1111,rob
+156,20,4.0627,126.72,-0.0442,0.0705,creA
+228,20,4.0471,131.94,-0.1408,0.0789,creB
+473,20,4.0254,128.01,+0.0023,0.0677,creC
+449,20,4.0871,128.66,+0.2082,0.0980,creD
+237,20,4.0729,132.54,-0.4970,0.0675,arcA
+45,15,3.5800,123.27,+0.7533,0.0222,yjjY
+227,20,4.0283,128.63,-0.0031,0.0573,yjtD
+
+
+Data files
+
+   None.
+
+Notes
+
+   None.
+
+References
+
+   Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and
+      aromaticity are the major trends of amino-acid usage in 999 Escherichia
+      coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a
+
+   Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga
+      maritima J Mol Evol. 54(5):563-8.
+
+   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
+   gbui           Calculates base usage indeces for protein-codin sequences
+   gcodoncompiler Calculates various kinds of amino acid and codon usage data
+
+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.
+