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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.

  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.

  sub gcskew{ 
     my $gb = shift; 
     my $window = shift; 
     my @gcskew = (); 
     return @gcskew; 
gcskewanalysisenglish.1285934592.txt.gz · Last modified: 2014/01/18 07:44 (external edit)