Thank you for your reply. I've already seen that post, but I'm not sure they can help me.

I have no knowledge of how to work with scripts and I think they don't totally fit my problem.

However in that page a guy posted this script

/#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::GenBank;
use Bio::SeqIO;

# get command-line arguments, or die with a usage statement
my $usage = "RetriveDataGenBank.pl Accessions_infile Fasta_outfilen";
my $infile = shift or die $usage;

my $outfile = shift or die $usage;
my $outfileformat = 'Fasta';
my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , -format => 'Fasta');
my @Acc_Numbers;

open (IN,$infile)||die;

my $line;

while ($line =[?]) {
  chomp $line;
  push (@Acc_Numbers, "'".$line."'")
}

my $seq_in = $gb->get_Stream_by_acc(@Acc_Numbers);
my $seq_out = Bio::SeqIO->new('-file' => ">$outfile",'-format' => $outfileformat); # write each entry in the input file to the output file

while (my $inseq = $seq_in->next_seq) { 
  $seq_out->write_seq($inseq);
}
exit

It seems to be fine for my problem but It gave me errors and I really don't know how to solve them

Unknown regexp modifier "/r" at prova.pl line 1, at end of line
"use" not allowed in expression at prova.pl line 1, at end of line
syntax error at prova.pl line 1, near "perl use strict"
BEGIN not safe after errors--compilation aborted at prova.pl line 1.