use strict;
use warnings;

#counting motifs

use Bio::SeqIO;
my $file = "SeqHisham.txt";
my $in = Bio::SeqIO->new(
        -format =>'fasta',
        -file   =>$file,
        );
my $motif_Count=0;
my $motif = 'ga';
while(my $seq = $in->next_seq){
        #since the sequence would be processed in a certain way convert to string
        my $string = $seq->seq;
        if($string=~/$motif/i){ #make the regex appropriate...
                $motif_Count++;
                }
        }
print "Found $motif_Count hits\n";