Re^2: Understanding a portion on the Perlretut

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Re^3: Understanding a portion on the Perlretut by Corion (Patriarch) on Dec 09, 2015 at 13:33 UTC
I linked to perlretut. Going there, I find: The naive regexp `...` [download] doesn't work; it may match a TGA , but there is no guarantee that the match is aligned with codon boundaries, e.g., the substring GTT GAA gives a match. A better solution is `while ($dna =~ /(\w\w\w)?TGA/g) { # note the minimal ? print "Got a TGA stop codon at position ", pos $dna, "\n"; }` [download] which prints `Got a TGA stop codon at position 18 Got a TGA stop codon at position 23` [download] Position 18 is good, but position 23 is bogus. What happened? Maybe it was too obvious for me, but a Codon is a nucleotide triplet.	[reply] [d/l] [select]

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Re^3: Understanding a portion on the Perlretut
by Corion (Patriarch) on Dec 09, 2015 at 13:33 UTC

I linked to perlretut. Going there, I find:

The naive regexp
    ...
[download]
doesn't work; it may match a TGA , but there is no guarantee that the match is aligned with codon boundaries, e.g., the substring GTT GAA gives a match. A better solution is
    while ($dna =~ /(\w\w\w)*?TGA/g) { # note the minimal *?
    print "Got a TGA stop codon at position ", pos $dna, "\n";
    }
[download]
which prints
    Got a TGA stop codon at position 18
    Got a TGA stop codon at position 23
[download]
Position 18 is good, but position 23 is bogus. What happened?

Maybe it was too obvious for me, but a Codon is a nucleotide triplet.

[reply]
[d/l]
[select]