Greetings, I'm working on a homework and I'm stuck with a part I just can't figure out. Today I asked another question and managed to solve that part, thanks to all who helped me on that occasion. Now, my problem is that I have printed the two genes I was supposed to find and now I'm supposed to print probes of length 6 with one mutation OF these 2 genes. These probes are supposed to be only explicit content of the 2 genes. A probe can't exist in the whole text and both of the genes. For example, a gene has CACTCT substring in it and that CACTCT should not be existent in the whole text and the other gene. Also CACTCT should have one letter different from the entire text. -mutations- my code is as below: 

$infile="input.txt";  

open(IN, "$infile") or die "can'topen \"$infile\"";    

$genom="";

while($line=<IN>)  
{
chomp $line;
$genom.=$line;


}
@allprobes=();
for($x=0;$x<=$alltextlength-6;$x++)
{
$all= substr $genom, $j, 6;
push(@allprobes,$all);

}
@probe=();


while($genom=~m/TATAAT.*?(ATG(...)*?(TAA|TAG|TGA))/g)
{
push (@gen, $1);

}

        $cnt = 0;
        $k=0;
        $m=0;
        
foreach $gen (@gen)
{
$length=length($gen);


    for($j=0; $j<$length-5; $j++)
    {
        $altilik= substr $gen, $j, 6;
        push (@probe,$altilik);



    while($allprobes[$m]=~m/$probe[$k]/g)
    {
        #push (@gen, $1);
        
        $cnt++;
        $k++;
    }
        $m++;

#print "@probe\n\n\n";
#print @allprobes;

    }

}


print "$cnt\n";

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In reply to finding probes with one mutation ? by hellworld

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