use strict;
use Data::Dumper;

my %hash=();
my ($key, $val);
while (<DATA>) {
    chomp;
    if (/^>(\w+)/) {
        if ($key) {$hash{$key} = $val}; 
        $key = $1; $val = "";
    } else {
        $val .= $_;
    }
}
$hash{$key} = $val; 
print Dumper \%hash;

__DATA__
>EP11110 (-) 
TGCAATCACTAGCAAGCTCTC
GCTGCCGTCACTAGCCTGTGG
>EP40005 (+) 
GGGGCTAGGGTTAGTTCTGGA
NNNNNNNNNNNNNNNNNNNNN