in reply to PERL STRING QUESTION

#!/usr/bin/perl -l

my $seq  = "atgtagat";
my $find = "gta";

my ($before, $after) = $seq =~ /(..)$find(..)/;

print "before: $before";    # "at"
print "after:  $after";     # "ga"

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Re^2: PERL STRING QUESTION
by AnomalousMonk (Archbishop) on Apr 01, 2010 at 08:20 UTC 
    my ($before, $after) = $seq =~ /(..)$find(..)/;

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    ... will find only one instance of a sub-sequence in a sequence. The following will find multiple instances of sub-sequences, either overlapping or non-overlapping: 

    >perl -wMstrict -le
"my $seq  = 'atggggtaggggat';
 my $find = 'ggg';
 print 'non-overlapping:';
 while ($seq =~ m{ (..) $find (..) }xmsg) {
   print qq{($1)$find($2)};
   }
 print 'overlapping:';
 while ($seq =~ m{ (?= (..) $find (..)) }xmsg) {
   print qq{($1)$find($2)};
   }
"
non-overlapping:
(at)ggg(gt)
(ag)ggg(at)
overlapping:
(at)ggg(gt)
(tg)ggg(ta)
(ta)ggg(ga)
(ag)ggg(at)

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