#!/usr/bin/perl

use strict;
use warnings;
use File::Find::Rule;
use Bio::FASTASequence::File;

my $directory = '/path/to/dir/';
my @fasta_files = File::Find::Rule->file->name( '*.fasta' )->in( $directory );

my $parser = Bio::FASTASequence::File->new;
for my $fasta_file ( @fasta_files ) {
    my $hashref = $parser->file( $fasta_file );

    for my $org ( keys %{$hashref} ) {
        print $org,"\n";

        my $sequence = $hashref->{$org}->getSequence;

        # search for anything in the sequence and get part of it...
    }
}