[Bioperl-l] Pattern search with gap

[Tamas Horvath]

And a slightly different code for multiple recognition:

my $seqstring ="--------------------CAAAATAAATAGGTTATACAGAAACA---------------------AGATAAAAATTACA--CAAG-AT-A----";
my $qseq    = "CAAGATA";

my @qqq = split (//,$qseq);
my $pat = join('-*', at qqq);

my $pat_rege = qr/$pat/;

while ($seqstring =~ /$pat_rege/g) {
my $before = $`;
my $match_seq = $&;
my $before_length = length $before;
my $mseq_length = length $match_seq;
my $start = 1 + $before_length;
my $end = $before_length + $mseq_length;
print "Start:$start End:$end\n";
}
#Start:45 End:72
#Start:84 End:92