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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 (http://www.g-language.org/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:

optiondescription
-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);
    }
}
g-basic.txt · Last modified: 2014/01/18 07:44 (external edit)