I think using File::Slurp is even easier and more perl-ish :)

use File::Slurp;

# read file as a string
my $text = read_file('dna.txt');

# now remove whitespace including line breaks
$text =~ s/\s+//g;

# ...do stuff

[download]
(update : removed a stray space)

In reply to Re^2: motif finding by RichardK
in thread motif finding by devi

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