Rahul Nayak
A Bioinformatician
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Perl script to find palindromic pattern !
By Rahul Nayak 2092 days ago
#!/usr/bin/perl
use strict;
use warnings;
use strict;
my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ];
my $in = do{ local $/; <DATA> };
chomp $in;
print $in;
for my $p1 ( 1 .. length( $in ) -2 ) {
next unless substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1 };
my $pals = 0;
for my $p2 ( 1 .. $p1 -1 ) {
last unless substr( $in, $p1-$p2, 1 ) eq $invert{ substr $in, $p1+$p2+1, 1 };
++$pals;
}
if( $pals ) {
my $val=substr( $in, $p1-$pals, ($pals+1)*2 );
my $st=$p1-$pals;
my $sLen=($pals+1)*2;
my $ed=($st+$sLen)-1;
print "$st\t$ed\t$sLen\t$val\n";
printf "%s%s at %d\n", ' 'x($p1-$pals),
substr( $in, $p1-$pals, ($pals+1)*2 ), $p1-$pals;
}
}
__DATA__
AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG
