I Would like to get some help. my program below is dicovering motifs by reading from a file. pi have generated motif and i am trying to match all the possible motifs with my sequence file.the motifs are well generated in lengths of 5,6.but i cannot get it to much the sequence and return the motif in the correct way and then calculate for only motifs that appear 90% in the background. Would anybody help?? Marrein

#Discovery of simple motifs in DNA sequences
#Input Files:Foreground sequences and background sequences.
#!/usr/bin/perl
#---------------------------------------------------------------------
+--
#initialize variables
#---------------------------------------------------------------------
+---

use strict;
use warnings;
my $fgcount;
my $count=0;
my $motif;
my @motifs='';  
my $dna ='';
my $seq='';
my $sequence='';
my $sequences='';
#my $line='';
my @dna = ( );
my $file = ' ';
my @file =( );
my @rna;
my $length ;
my $combinations ;
my $combinations2 ;
my $counter;

$seq='foreground_faa.txt';
#-------------------------------------------
#subroutine to open file for readability
#-------------------------------------------
sub get_file{
@dna = @_;

    unless (open(IFILE, $seq)) {
       print "could not open file sequence!\n";
          exit;
  }
@dna = <IFILE>;
close IFILE;
return @dna;
}

#--------------------------------------------   
#main program.
#--------------------------------------------

 get_file($seq); 
 $file=extract_sequence(@dna);
 join_seq($sequence);
 create_motif($combinations);
 create_motif2($combinations2);
 get_all_motifs(@motifs);
 #get_motif(@file);
 #get_motif($dna); 

#--------------------------------------------   
#subroutine to extract seq from header file
#--------------------------------------------
  sub extract_sequence  {
#initialize variables
   @dna=@_;
   $sequence='';
   
       
  
  foreach my $line (@dna){
  if ($line =~ /^\s*$/) { #discard blank line
      next;
       }elsif ($line =~ /^>/){ #discard fasta header
         next;
          }else {                   
           $sequence .=$line;
            }
           }

#print $sequence,"\n";
 return $sequence;

}
#--------------------------------
#Subroutine to join sequences
#--------------------------------
 sub join_seq {

@file = split ('',$file);
#print @file, "\n";
return @file;
 }

#---------------------------------------------------------------------
+---------
#Subroutines to discover motifs of the lenghth 5
#---------------------------------------------------------------------
+---------
sub create_motif {  #creates avery possible 5-mer

my $base = join ",", qw/A T C G/;
my $L = 5;
#my $L2 = 6;
my $string = "{$base}" x $L;
my $combinations = glob $string;

#print join ":", $combinations;
return join ":", $combinations;
}  

#---------------------------------------------------------------------
+---------
#Subroutines to discover motifs of the lenghth 6
#---------------------------------------------------------------------
+---------

sub create_motif2 {  #creates every possible 6-mer

 my $base2 = join ",", qw/a t c g/;
 my $L2 = 6;
 my $string2 = "{$base2}" x $L2;
 my $combinations2 = glob $string2;

#print join ":", $combinations2;
return join ":", $combinations2;
     }

#---------------------------------------------------------------------
+-
#subroutine check all the available motifs in the file
#---------------------------------------------------------------------
+- 
sub get_all_motifs { 

$combinations=$combinations2;
@motifs=$combinations;
print @motifs; 
return @motifs;
}

foreach  $combinations (@motifs){
   foreach $sequence(@file)  {
     if($sequence =~/$combinations/){
      $counter++;
    }
   }
                                                          
     print $sequence;
     return $sequence;
      #exit;
            }

#---------------------------------------------------------------------
+-
#subroutine check all the available motifs in the file
#---------------------------------------------------------------------
+-    
sub calculate_percentage  {
#my $percentage;

   my $percentage = $counter / scalar(@file);
     print "$percentage is ";
   
      if ($percentage =>90);
          
       #print $motif;
       #return $motif_sequences;    
        
}
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