Question

I was assigned a problem to find genes when given a string of the letters A,C,G, or T all in a row, like ATGCTCTCTTGATTTTTTTATGTGTAGCCATGCACACACACACATAAGA. A gene is started with ATG, and ends with either TAA, TAG, or TGA (the gene excludes both endpoints). The gene consists of triplets of letters, so its length is a multiple of three, and none of those triplets can be the start/end triplets listed above. So, for the string above the genes in it are CTCTCT and CACACACACACA. And in fact my regex works for that particular string. Here’s what I have so far (and I’m pretty happy with myself that I got this far):

(?<=ATG)(([ACGT]{3}(?<!ATG))+?)(?=TAG|TAA|TGA)

However, if there is an ATG and end-triplet within another result, and not aligned with the triplets of that result, it fails. For example:

Results for TCGAATGTTGCTTATTGTTTTGAATGGGGTAGGATGACCTGCTAATTGGGGGGGGGG :
TTGCTTATTGTTTTGAATGGGGTAGGA
ACCTGC

It should find also a GGG but doesn’t: TTGCTTATTGTTTTGA(ATG|GGG|TAG)GA

I’m new to regex in general and a little stuck…just a little hint would be awesome!

Answer 1

Here’s a possible regex:

(?=(ATG((?!ATG)[ATGC]{3})*(TAA|TAG|TGA)))

A little test-rig:

public class Main {
    public static void main(String[]args) {
        String source = "TCGAATGTTGCTTATTGTTTTGAATGGGGTAGGATGACCTGCTAATTGGGGGGGGGGATGATGTAG";
        Matcher m = Pattern.compile("(?=(ATG((?!ATG)[ATGC]{3})*(TAA|TAG|TGA)))").matcher(source);
        System.out.println("source : "+source+"\nmatches:");
        while(m.find()) {
            System.out.print("         ");
            for(int i = 0; i < m.start(); i++) {
                System.out.print(" ");
            }
            System.out.println(m.group(1));
        }
    }
}

which produces:

source : TCGAATGTTGCTTATTGTTTTGAATGGGGTAGGATGACCTGCTAATTGGGGGGGGGGATGATGTAG
matches:
             ATGTTGCTTATTGTTTTGAATGGGGTAGGATGACCTGCTAATTGGGGGGGGGGATGA
                                ATGGGGTAG
                                          ATGACCTGCTAA
                                                                     ATGTAG