g basic

An introduction of G-language GAE

Step 0 - Install

Users can simply download G-language GAE package either from the KNOB Project (http://knob.sourceforge.jp/en/) or the project official page (https://github.com/gaou/g-language/wiki). Follow README file for installing the package.

Step 1 - Start

Let's begin with a GenBank file of Bacillus subtilis ("bsub.gbk"). To load the bsub.gbk into G instance just write in following lines.

  use G;
  $gb = load("bsub");

Save this script as test.pl then execute it in shell as follow.

  perl test.pl  [ENTER]

The output should look like this with loaded G-language.

              __/__/__/__/__/__/__/__/__/__/__/__/__/
  
                      G-language System
  
               Version: 1.6.10 
  
               Copyright (C) 2001-2007 G-language Project
               Institute of Advanced Biosciences,
               Keio University, JAPAN
  
                  http://www.g-language.org/
  
              __/__/__/__/__/__/__/__/__/__/__/__/__/
  
  
   Accession Number: AL009126
  
   Length of Sequence :   4214814
            A Content :   1187757 (28.18%)
            T Content :   1192867 (28.30%)
            G Content :    915023 (21.71%)
            C Content :    919167 (21.81%)
               Others :         0 (0.00%)
           AT Content :    56.48%
           GC Content :    43.52%

Step 2 - Use of standard function (1)

In this section we will demonstrate how to analyze codon usage for each genes using G-language GAE. Just add a single line into script used in Step 1. This script will display codon usage with a codon table.

  use G;
  $gb = load ("bsub");
  codon_usage($gb);

Step 3 - Use of standard functions (2)

The function codon_usage() perform analysis of codon usage. The codon_usage() has three types of options:

option	description
-CDSid	This sets specific gene ID to analyze (default: whole gene)
-output	This sets directory for output. 'stdout' is for standard output, 'f' is for saving to given file (default: 'stdout')
-filename	This sets file name (default: 'codon_usage.csv')

These options are described as following syntax.

  codon_usage($gb, -output=>'f', -filename=>'bsub_CodonUsage.csv');

Put '-' in the head of option name and join option and value with '=>'.

For calculating specific gene, such as 'CDS113' which codes gene for elongation factor, type as follow.

  use G;
  $gb = load("bsub");
  codon_usage($gb, -CDSid=>'CDS113');

Step 4 - For further study

G-language GAE provide users not only various functions for genome analysis but also platforms for genome databases. The platform includes functions invokable from G instance such as process for each genes, start and stop codon, and process for intron and exon.

For example, $gb->cds() returns all CDSs in a genome. Using this function, The step 3 script can be rewritten as this:

  use G;
  $gb = load("bsub");
  
  foreach $cds ($gb->cds()){
      if($gb->{$cds}->{gene} =~ /tufA/){
  	codon_usage($gb, -CDSid=>$cds);
      }
  }