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gcskewanalysisenglish [2010/10/01 12:04]
gcskewanalysisenglish [2014/01/18 07:44]
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-====== Introduction ====== 
-As a beginning of this series of tutorial (‘GCskew Basics’), we analyzed GC skew by using only existing G-language GAE methods. In this tutorial as a next step, we are going to analyze actual GC skew by taking advantage of G-language GAE and Perl scripts. 
-====== STEP 1 - Loading G and subroutines ====== 
-Let’s start with writing Perl scripts. First create new G instance as shown in previous tutorial. 
-<code perl> 
-  use G; 
-  my $gb = load("​ecoli"​);​ 
-There will be no need to suffer from loading genome files, parsing it, or searching for which functions to use when G-language GAE is selected. The above two-line script is it. Therefore users can focus on what they want not programming itself. 
-Here we are going to make script with GC skew subroutine to avoid re-build same program. The subroutine returns value of GC skew as output. Setting secondary argument as window size makes script much more resourcefull. 
-<code perl> 
-  sub gcskew{ ​ 
-     my $gb = shift; ​ 
-     my $window = shift; ​ 
-     my @gcskew = ();  
-      ​ 
-     ​return @gcskew; ​ 
-  }  
-====== STEP 2 - Calculation and output of GC skews ====== 
gcskewanalysisenglish.txt · Last modified: 2014/01/18 07:44 (external edit)