This is not what you want to use to capture the output from a command; for that you should use merely backticks or qx//, as described in `STRING` in perlop.

##</code><code>##

#!usr/bin/perl
use say;
use strict;
use warnings;

my $dir_before = `ls -la`;
chomp $dir_before;
say $dir_before;

# execute your linux command with backticks
`blastn -query example.fa -db /home/tinyos/blast_db/refseq_rna.00 -out results.txt`;

my $dir_after = `ls -la`;
chomp $dir_after;
say $dir_after;

__END__

$ perl bio.pl
total 20
drwxr-xr-x 2 tinyos tinyos 4096 Jun 28 00:30 .
drwxr-xr-x 7 tinyos tinyos 4096 Jun 28 00:19 ..
-rw-r--r-- 1 tinyos tinyos  279 Jun 28 00:30 bio.pl
-rw-r--r-- 1 tinyos tinyos    0 Jun 28 00:21 bio.pl~
-rw-r--r-- 1 tinyos tinyos  459 Jun 28 00:04 example.fa
-rw-r--r-- 1 tinyos tinyos  458 Jun 28 00:04 example.fa~
total 32
drwxr-xr-x 2 tinyos tinyos  4096 Jun 28 00:30 .
drwxr-xr-x 7 tinyos tinyos  4096 Jun 28 00:19 ..
-rw-r--r-- 1 tinyos tinyos   279 Jun 28 00:30 bio.pl
-rw-r--r-- 1 tinyos tinyos     0 Jun 28 00:21 bio.pl~
-rw-r--r-- 1 tinyos tinyos   459 Jun 28 00:04 example.fa
-rw-r--r-- 1 tinyos tinyos   458 Jun 28 00:04 example.fa~
-rw-r--r-- 1 tinyos tinyos 10739 Jun 28 00:30 results.txt