hey i have a code (given below) which counts A,T,G,C and GC,and GC percentage in between 0-200, 1-201, 2-202 regions. But i have to count a lenghty sequence upto 10,000 basepairs, so this would be very lenghty and less efficient. What modification can i do in this code so that it can automateically count upto 10,000 bases.

#!/usr/bin/perl

use warnings;my$seq;my$file;my$line;my$len;my@seq;

print "Select the region where you want to find CpG Island\n";

print  "1. Region 1-200\n";

print  "2. Region 2-202\n";

print  "3. Region 3-203\n";    

$choice =<STDIN>;

chomp($choice);

if($choice == 1){

&region1;

}

if($choice == 2){

&region2;

}

if($choice == 3){

&region3;

}



    sub region1 {

$file = 'd:\perl\1.txt';

open(INPUT, $file) or die ("File not found");

foreach($line = <INPUT>){

$a = substr($line,0,200) =~tr/A//;

$t = substr($line,0,200) =~tr/T//;

$g = substr($line,0,200) =~tr/G//;

$c = substr($line,0,200) =~tr/C//;

$cg = substr($line,0,200) =~tr/ CG //;

$total = substr($line,0,200) =~tr/ATGC//;

}

$CpG = ($cg)/$total*100;

print"Count of A = $a\n";

print"Count of T = $t\n";

print"Count of G = $g\n";

print"Count of C = $c\n";

print"CG = $cg\n";

print"total count of ATGC = $total\n";

print"CpG percentage = $CpG\n";

if ($CpG>=60){



print"CpG present";}



else{ print"CpG absent";}

}



    sub region2 {

$file = 'd:\perl\1.txt';

open(INPUT, $file) or die ("File not found");

foreach($line = <INPUT>){

$a = substr($line,1,201) =~tr/A//;

$t = substr($line,1,201) =~tr/T//;

$g = substr($line,1,201) =~tr/G//;

$c = substr($line,1,201) =~tr/C//;

$total = substr($line,1,201) =~tr/ATGC//;

}

$CpG = ($g+$c)/$total*100;
regarding perl,So i need your help for the same.

print"Count of A = $a\n";

print"Count of T = $t\n";

print"Count of G = $g\n";

print"Count of C = $c\n";

print"total count of ATGC = $total\n";

print"CpG percentage = $CpG\n";

if ($CpG>=60){



print"CpG present";}



else{ print"CpG absent";}

 }

    sub region3 {

$file = 'd:\perl\1.txt';

open(INPUT, $file) or die ("File not found");

foreach($line = <INPUT>){

$a = substr($line,2,203) =~tr/A//;

$t = substr($line,2,203) =~tr/T//;

$g = substr($line,2,203) =~tr/G//;

$c = substr($line,2,203) =~tr/C//;

$total = substr($line,2,203) =~tr/ATGC//;

}

$CpG = ($g+$c)/$total*100;

print"Count of A = $a\n";

print"Count of T = $t\n";

print"Count of G = $g\n";

print"Count of C = $c\n";

print"total count of ATGC = $total\n";

print"CpG percentage = $CpG\n";

if ($CpG>=60){



print"CpG present";}



else{ print"CpG absent";}

}
[download]