Hello fellow monks!
I have a project in which I need to read some DNA sequences and check if they start with 'ATG' and end in 'TAA', 'TAG' or 'TGA'. If not, I am supposed to find the desired substring within the original sequence.
Imagine the following string:

GTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAAGGGCAGGTAG
+CGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTGGCGATGATTGAAAAAACTATCGGCG
+GTCAGGATGCTTTGCCGAATATCAGCGATGCCGAACGTATTTTTTCTGACCTGCTCGCAGGACTTGCCA
+GCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAAC
+ATGTTCTGCATGGTATCAGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTG
+GCGAAAAAATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGGTGATTG
+ATCCGGTAGAAAAATTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCGGAATCGACTC
+GCCGTATCGCCGCCAGCCAGATCCCAGCCGATCACATGATCCTGATGGCGGGCTTTACCGCCGGTAATG
+AAAAGGGTGAACTGGTGGTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTT
+TACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGTCAGGTGC
+CGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAG
+TCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTA
+ATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTACCAGTTAAAGGGATCT
+CTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGG
+CGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGT
+ACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGCGCGCGTGCCCGCCGTGCGATGCAGGATGAGTTCT
+ATCTGGAGCTGAAAGAGGGGCTGCTGGAGCCGCTGGCGGTTACGGAGCGGTTGGCGATTATCTCTGTTG
+TCGGCGACGGTATGCGCACGCTACGCGGCATTTCAGCGAAATTCTTCGCCGCGCTGGCGCGGGCCAATA
+TCAATATCGTGGCGATCGCTCAGGGATCTTCTGAGCGTTCCATTTCTGTGGTGGTGAATAACGACGATG
+CCACCACCGGCGTGCGGGTAACGCACCAGATGCTGTTCAATACCGATCAGGTGATTGAAGTGTTTGTCA
+TTGGCGTCGGCGGCGTCGGCGGCGCGCTACTGGAACAGCTTAAACGTCAGCAAACCTGGTTGAAGAACA
+AGCACATCGATCTACGCGTGTGCGGCGTGGCGAACTCAAAGGCGTTGCTAACCAATGTGCATGGCCTGA
+ATCTGGACAACTGGCAGGCGGAACTGGCGCAAGCGAACGCGCCGTTCAATCTGGGACGCTTAATTCGCC
+TGGTGAAAGAATATCATCTACTCAATCCGGTGATTGTTGATTGCACCTCCAGTCAGGCGGTGGCCGACC
+AGTATGCTGACTTCCTGCGTGAAGGATTCCATGTGGTGACGCCAAACAAGAAAGCGAACACCTCGTCGA
+TGGACTACTACCATCAGCTACGTTTCGCCGCCGCGCAATCACGGCGCAAATTCTTGTATGACACCAACG
+TCGGCGCCGGTTTGCCGGTAATCGAAAACCTGCAAAACCTGCTGAATGCGGGTGATGAACTGCAAAAAT
+TTTCCGGCATTCTTTCCGGGTCGCTCTCTTTTATTTTCGGTAAACTGGAAGAGGGGATGAGTCTCTCAC
+AGGCGACCGCCCTGGCGCGCGAGATGGGCTATACCGAACCCGATCCGCGCGACGATCTTTCCGGTATGG
+ATGTGGCGCGGAAACTGTTGATCCTCGCCCGCGAGACGGGCCGCGAGCTGGAGCTTTCCGATATTGTGA
+TTGAACCGGTGTTGCCGGACGAGTTTGACGCCTCCGGCGATGTGACCACCTTTATGGCGCATCTGCCGC
+AGCTTGACGACGCGTTTGCCGCCCGTGTGGCGAAAGCTCGTGATGAAGGTAAGGTATTGCGCTATGTGG
+GCAATATCGAAGAGGATGGCGTGTGCCGCGTGAAGATTGCCGAAGTTGATGGTAACGATCCGCTCTTCA
+AAGTGAAAAACGGTTAAGAAAACGCGCTGGCGTTCTACAGCCACTATTATCAGCCCTTGCCGTTGGTGC
+TGCGCGGCTACGGCGCAGGCAATGATGTGACGGCGGCGGGCGTGTTTGCCGATCTGTTACGGACCCTCT
+CATGGAAGTTAGGAGTT
[download]

where 'ATG' and 'TAA' are somewhere within it but now in the start and end positions, as they should.
For finding the correct start position, I suppose I could do:

$seq='GTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAAGGGC
+AGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTGGCGATGATTGAAAAAACTA
+TCGGCGGTCAGGATGCTTTGCCGAATATCAGCGATGCCGAACGTATTTTTTCTGACCTGCTCGCAGGAC
+TTGCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGA
+TCAAACATGTTCTGCATGGTATCAGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTT
+GCCGTGGCGAAAAAATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGG
+TGATTGATCCGGTAGAAAAATTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCGGAAT
+CGACTCGCCGTATCGCCGCCAGCCAGATCCCAGCCGATCACATGATCCTGATGGCGGGCTTTACCGCCG
+GTAATGAAAAGGGTGAACTGGTGGTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCG
+CCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGTC
+AGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCG
+CCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATA
+CCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTACCAGTTAAAG
+GGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGA
+TGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCT
+CTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGCGCGCGTGCCCGCCGTGCGATGCAGGATG
+AGTTCTATCTGGAGCTGAAAGAGGGGCTGCTGGAGCCGCTGGCGGTTACGGAGCGGTTGGCGATTATCT
+CTGTTGTCGGCGACGGTATGCGCACGCTACGCGGCATTTCAGCGAAATTCTTCGCCGCGCTGGCGCGGG
+CCAATATCAATATCGTGGCGATCGCTCAGGGATCTTCTGAGCGTTCCATTTCTGTGGTGGTGAATAACG
+ACGATGCCACCACCGGCGTGCGGGTAACGCACCAGATGCTGTTCAATACCGATCAGGTGATTGAAGTGT
+TTGTCATTGGCGTCGGCGGCGTCGGCGGCGCGCTACTGGAACAGCTTAAACGTCAGCAAACCTGGTTGA
+AGAACAAGCACATCGATCTACGCGTGTGCGGCGTGGCGAACTCAAAGGCGTTGCTAACCAATGTGCATG
+GCCTGAATCTGGACAACTGGCAGGCGGAACTGGCGCAAGCGAACGCGCCGTTCAATCTGGGACGCTTAA
+TTCGCCTGGTGAAAGAATATCATCTACTCAATCCGGTGATTGTTGATTGCACCTCCAGTCAGGCGGTGG
+CCGACCAGTATGCTGACTTCCTGCGTGAAGGATTCCATGTGGTGACGCCAAACAAGAAAGCGAACACCT
+CGTCGATGGACTACTACCATCAGCTACGTTTCGCCGCCGCGCAATCACGGCGCAAATTCTTGTATGACA
+CCAACGTCGGCGCCGGTTTGCCGGTAATCGAAAACCTGCAAAACCTGCTGAATGCGGGTGATGAACTGC
+AAAAATTTTCCGGCATTCTTTCCGGGTCGCTCTCTTTTATTTTCGGTAAACTGGAAGAGGGGATGAGTC
+TCTCACAGGCGACCGCCCTGGCGCGCGAGATGGGCTATACCGAACCCGATCCGCGCGACGATCTTTCCG
+GTATGGATGTGGCGCGGAAACTGTTGATCCTCGCCCGCGAGACGGGCCGCGAGCTGGAGCTTTCCGATA
+TTGTGATTGAACCGGTGTTGCCGGACGAGTTTGACGCCTCCGGCGATGTGACCACCTTTATGGCGCATC
+TGCCGCAGCTTGACGACGCGTTTGCCGCCCGTGTGGCGAAAGCTCGTGATGAAGGTAAGGTATTGCGCT
+ATGTGGGCAATATCGAAGAGGATGGCGTGTGCCGCGTGAAGATTGCCGAAGTTGATGGTAACGATCCGC
+TCTTCAAAGTGAAAAACGGTTAAGAAAACGCGCTGGCGTTCTACAGCCACTATTATCAGCCCTTGCCGT
+TGGTGCTGCGCGGCTACGGCGCAGGCAATGATGTGACGGCGGCGGGCGTGTTTGCCGATCTGTTACGGA
+CCCTCTCATGGAAGTTAGGAGTT';
if($seq=~/.*(ATG.*)/) {$substring_with_correct_start=$1;}
[download]

What could I do to find the correct ending of the string, i.e., to end in either 'TAA', 'TAG' or 'TGA'? This part is troubling me, since there could me more than one correct codes as endings...

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