Re: Perl regular expression for amino acid sequence

This will come close, but will fail if the match is followed by extra repetitions.

/(?:(?!(.)\1\1)[QGYN]){3,6}/;
[download]

You might have to consider each character separately, which leads to a long ugly string of alternations. The first char matches your character class. The second is either not a repeat, or is a repeat followed by not a repeat. The third is either not a repeat of the second, or a repeat followed by not a repeat.

After that, the pattern is repeated for the 4th and 5th characters, but they're all optional and nested (so if you don't have the 4th char, you don't look for the 5th). The 6th char doesn't need to check for repetitions, because it was checked by the pattern for the 5th char.

while ($seq{$k} =~ /(([QGYN])
                   ((?!\2)[QGYN]|\2(?!\2))
                   ((?!\3)[QGYN]|\3(?!\3))
                   (?:((?!\4)[QGYN]|\4(?!\4))
                      (?:((?!\5)[QGYN]|\5(?!\5))
                         [QGYN]?)?)?)
                   /xg) {
print "\n$k";
print $1." begins at position ", (pos($seq{$k})-length($s)) , "\n";
}
[download]

Update: adjusted to fit OP's code snippet.
Update2: As Ikegami noted (and I noted in responding to a different post), this solution has the problem of looking too far ahead. It won't take the first two characters out of a trio. A working regex-only solution is posted as a reply to this post.

Caution: Contents may have been coded under pressure.

Comment on Re: Perl regular expression for amino acid sequence Select or Download Code

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Re^2: Perl regular expression for amino acid sequence by Roy Johnson (Monsignor) on Dec 01, 2004 at 21:45 UTC
Here's a pure regex solution that works: use strict; use warnings; while(<DATA>) { print "$_---\n"; my $m; while (/([QGYN]{2} # First two characters of the desired class (?: # Followed by the complex expression... # Lookback at the previous two chars (?<=(.)(.)) # Check that the next char differs from at least one of th +em (?:(?!\2)\|(?!\3)) [QGYN] # Then take another of the desired class ){1,4} # ...1 to 4 times )/gx) { $m = $1; printf "---> $m starting at %d\n", pos($_)-length($m); } print "=====\n"; } __DATA__ QYGNGNG GGGGGNYGNQYNNNQGYQ QGYNNN xxxxxxxGNNNxxxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx [download] Caution: Contents may have been coded under pressure.	[reply] [d/l]
Re^3: Perl regular expression for amino acid sequence by hv (Prior) on Dec 02, 2004 at 13:34 UTC
This is a very nice solution, I haven't seen that trick before. Hugo	[reply]
Re^2: Perl regular expression for amino acid sequence by dragonchild (Archbishop) on Dec 01, 2004 at 20:47 UTC
Build that programmatically. `my $regex = '(([QGYN])'; $regex .= '((?!\\' . $_ . ')[QGYN]\|\\' . $_. '(?!\\${_}))' for 2 .. 3; $regex .= '(?:((?!\\' . $_ . ')[QGYN]\|\\' . $_ . '(?!\\' . $_ . '))' f +or 4 .. 5; $regex .= '[QGYN]?)?)?)'; $regex = qr/$regex/; while ($seq{$k} =~ /$regex/g) { print "\n$k"; print $1." begins at position ", (pos($seq{$k})-length($s)) , "\n" +; }` [download] Now, I have no idea what all that does, but it's easily broken apart. :-) Being right, does not endow the right to be rude; politeness costs nothing. Being unknowing, is not the same as being stupid. Expressing a contrary opinion, whether to the individual or the group, is more often a sign of deeper thought than of cantankerous belligerence. Do not mistake your goals as the only goals; your opinion as the only opinion; your confidence as correctness. Saying you know better is not the same as explaining you know better.	[reply] [d/l]
Re^2: Perl regular expression for amino acid sequence by ikegami (Patriarch) on Dec 01, 2004 at 21:11 UTC
Input `'xxxxxxxGNNNxxxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx'` gives: `NNGYGY begins at position 19 GYGYNN begins at position 32 NNGN begins at position 47` [download] rather than `GNN begins at position 7 <--- NNGYGY begins at position 19 GYGYNN begins at position 32 NNGNN begins at position 47 <---` [download]	[reply] [d/l] [select]
Re^2: Perl regular expression for amino acid sequence by seaver (Pilgrim) on Dec 01, 2004 at 20:27 UTC
Thank you! It sure did work, and it was surely surprising that it was so ugly. :-D Sam	[reply]


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