Off topic:Finding The Count And Location Of Two Substring In Two Different File Present In The Same Location.

Question

[Jamis]

From a given two sequences i need to check for every three codons and if the changes are same as in the following list, then i ve to check out the location of changes and the codons which are changed and count their number of occurences.

For eg:

seq1- TTCAUUUCCCAU
seq2- TTTAUAUCGCAC

so, the output which i need to get is:

TTC->TTT considered / location-1 / count-1
AUU->AUA considered / location-2 / count-1 
UCC->UCG considered / location-3 / count-1

NOTE:

CAU->CAC not considered because it is not there in the following list

LIST:-> The direction of changes should also be considered.

first sequence->second sequence

TTC->TTT
CTG->UUA
AUU->AUA
GUG->GUA
UCC->UCG
CCC->CCG
ACC->ACG
GCC->GCG
UAC->UAU
UGA->UAG
CAC->CAU
CAG->CAA
AAC->AAU
AAG->AAA
GAC->GAU
GAG->GAA
UGC->UGU
CGG->CGU
AGC->AGU
AGG->CGU
AGA->CGU
UAA->UAG
GGC->GGU

and the code which i ve written till now is :

#!/usr/bin/perl
print"Enter the sequence:";
$a=<>;
print"Enter the mutated sequence:";
$b=<>;
chomp($a);
chomp($b);
my @codon=split(/(\w{3})/,$a);
my @codon1=split(/(\w{3})/,$b);
open(OUT,">output.txt") or die;
$count=0;
@new=();
@new1=();
for($i=0;$i<=$#codon;$i++)
    {
      for($j=0;$j<=$#codon1;$j++)
        {
         if($codon[$i]={TTC}) || ($codon1[$j]={TTT})
            {
             $count++;
            }
         }
     }
print OUT " @new";
close OUT;