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

Initial upload

                                      gcai
Function

   Calculate codon adaptation index for each gene

Description

   gcai calculates codon adaptation index (CAI) for each gene. CAI is measure
   a of the relative adaptiveness of the codon usage of a gene towards the
   codon usage of highly expressed genes, ranging from 0 (no bias) to 1
   (maximum bias). CAI can be used as a 'universal' measure of codon usage
   bias as it is correlated with various gene features such as gene expression
   level, GC content, and GC skew.

   The CAI for a gene where A(i) is the amino acid at position i and W(A) is
   the W value corresponding to the amino acid is calculated as follows:

   CAI = sum(log(e,W(A(i))))

   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 gcai

% gcai refseqn:NC_000913
Calculate codon adaptation index for each gene
Codon usage output file [nc_000913.gcai]: 

   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    [*.gcai] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include when translating using standard
                                  codon table
   -wabsent            string     [-1] W value of codons absent from a
                                  reference set to negative when excludes such
                                  codons from the calculation (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

   gcai reads one or more nucleotide sequences.

Output file format

   The output from gcai is to a plain text file.

   File: nc_000913.gcai

Sequence: NC_000913
cai,gene
0.7256,thrL
0.4831,thrA
0.4719,thrB
0.5178,thrC
0.4989,yaaX
0.4933,yaaA
0.4533,yaaJ
0.7074,talB

   [Part of this file has been deleted for brevity]

0.4681,yjjX
0.4797,ytjC
0.5350,rob
0.4932,creA
0.3918,creB
0.4170,creC
0.4167,creD
0.6466,arcA
0.4236,yjjY
0.3913,yjtD


Data files

   None.

Notes

   None.

References

   Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional
      synonymous codon usage bias, and its potential applications.
      Nucleic Acids Res. 15(3):1281-95.

   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

   gp2  Calculate the P2 index of each gene
   gphx Identify predicted highly expressed 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.