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g-basic [2010/11/17 22:07]
ike
g-basic [2010/11/23 11:08]
gaou
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 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. 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 ===== ===== Step 1 - Start =====
  
-Let's begin with a genbank ​file of Bacillus subtilis ("​bsub.gbk"​).+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. To load the bsub.gbk into G instance just write in following lines.
  
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                ​Others :         0 (0.00%)                ​Others :         0 (0.00%)
            AT Content :    56.48%            AT Content :    56.48%
-           GC Content :    43.52%===== Step 2 - Use of standard function (1) =====+           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. 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. Just add a single line into script used in Step 1.
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   $gb = load ("​bsub"​);​   $gb = load ("​bsub"​);​
   codon_usage($gb);​   codon_usage($gb);​
-===== Step 3 - Use of standard ​function ​(2) =====+ 
 +===== Step 3 - Use of standard ​functions ​(2) =====
  
 The function codon_usage() perform analysis of codon usage. The function codon_usage() perform analysis of codon usage.
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 ===== Step 4 - For further study ===== ===== 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)