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g-basic [2010/11/17 22:08]
ike
g-basic [2014/01/18 07:44]
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-====== 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) ===== 
- 
- 
-===== 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 function (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);​ 
-      } 
-  } 
- 
  
g-basic.txt ยท Last modified: 2014/01/18 07:44 (external edit)