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3.3. Searching for start and stop codons
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We have written an algorithm for finding genes. But you remember that we arestill to write the two functions for finding the next stop codonand the next start codon. Let's see how we can do that. We are looking for triplets. We use the term triplets as long as wehave no proof that they are codons. You can have triplets outside genes. Within genes, they are called codons. In general, we arelooking for triplets. If you have a sequence like thisone and you are looking for occurrences of this triplet, whatyou have to do is: position your triplet at the beginning of the sequence. Compare the first letter. If it is not the same, skip tothe second triplet, this one. Make the comparison. Again here, the first comparison works. So, you may do the second comparison, it works. But the third doesn't. Again, you progress and then youhave, here, a match, a second match and a third match. So, you have found an occurrence of the triplets on the sequence. That means that the number of comparisons, in the worst case, for one of the three stop codonsis the length of the text.
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