Question

I am using perl and regular expression to find an ORF (open reading frame) with a minimal size of 45 bases using.
Basically it means:
Find a substring a string that is composed ONLY of the letters ATGC (no spaces or new lines) that:

1. Starts with “ATG”
2. ends with “TAG” or “TAA” or “TGA”,
3. is at least 39 chars long
4. is dividable by 3

My first code was:

$CDSString = "ATGCACACACACACACACACACACACACACACACACACACACACACACACACACACATGA";
if($CDSString =~ m/(ATG.{45,}(TAG|TAA|TGA))/) 
{
    my $CDSCurrent = $1;
    if ((length($CDSCurrent) % 3) == 0)
    { 
        # do something
    }
}

which works fine, but I thought there might be a better way.
So I tried:

$CDSString = "ATGCACACACACACACACACACACACACACACACACACACACACACACACACACACATGA";
if ($CDSString =~ m/ATG(...){13,}(TAG|TAA|TGA)/ )
{
    # do something
}

but for some reason it doesn’t match the string above it, and I can’t figure out why.
Can anyone figure it out? Thank you in advance.

Answer 1

Your regex is not making sure that everything between the start and stop codons is in fact composed of the letters ATGC only. You should be using:

if ($CDSString =~ m/ATG(?:[ATGC]{3}){13,}(?:TAG|TAA|TGA)/i) {...}

(But your original regex works, too, it just won’t reject invalid matches. So there may be another problem somewhere else.)