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

Initial upload

                                     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.