Hi to all Monks,

I am trying to find the common patterns in different strings. I used the KMP algorithm. It works best for a single string but show almost nothing for the same string in next iterator of loop, Here is my code

use CGI qw(:standard);
use strict;

print   header;



BEGIN{ push @INC,'C:/src/String-1.5','C:/src/bioperl-live','C:/src/ens
+embl/modules','C:/src/ensembl-compara/modules','C:/src/ensembl-variat
+ion/modules','C:/src/ensembl-functgenomics/modules','C:/src/DBD-mysql
+-4.021';};

use strict;
use warnings;
use string;
my $T_one='GAATTCACGGATAGCCWGGTACGATGATAGATGAATTCGACTAGAATGCCWGGAAGAAT
+gGAATTC';
my $Ta='GAATTCACGGATAGCCWGGTACGATGATAGATGAATTCGACTAGAATGCCWGGAAGAATgGA
+ATTC';
my $rr='GAATTCACGGATAGCCWGGTACGATGATAGATGAATTCGACTAGAATGCCWGGAAGAATgGA
+ATTC';
my @P=('GAATTC','CCWGG');
my @next;
my @loc;
my $m;
my $l=0;
my $lt;my $T;
my @text=(0);
my @tt=($T_one,$Ta,$rr);

for(my $i=0;$i<3;$i++){  $T=$tt[$i];

    @loc=();
    print "<\br>";  
                
    @text=();
         my $str = new String($T);   # USE  OF STRING MODULE TO FETCH 
+THE SEQUENCE
        print  "length of gene sequence array     ", $lt= $str->length
+, "\n";    # LENGTH OF THE SEQUENCE
          $lt= $str->length;
          my $z=0;                         # FOR ARRAY INCREMENT
              for(my $k=0; $k<$lt;$k++){
                   $text[$z]=$str->charAt($k);   #ASSIGNING THE ARRAY 
+OBJECT VALUES TO AN ARRAY
                  $z++;
                 } #END OF FOR LOOP
                
            
        foreach my $P(@P){
                        print knuth_morris_pratt($T,$P);
                        print"\n";
                        }
                        
                
                
                
                @loc = sort {$a <=> $b} @loc;
                print"</br>";print "@loc";print "</br>";
                

                my $i=0;
                        for(my $k=0;$k<$lt;$k++){
                            print $i;
                            if ($k == $loc[$i]){ 
                                print "<span style=background-color:re
+d;>" .  $text[$k] . "</span>";
                                $i++;
                                 
                            }
                            else
                            { print $text[$k];
                                
                            }
                        }  # end of $k for loop

#print"\n";print "@loc";print "<\n>";
                         # FOR ARRAY INCREMENT
              print "</br>";
}   #end of $T for each loop











sub knuth_morris_pratt_next {
    my ( $P ) = @_; # The pattern.
    use integer;
    $m=length $P;
    my ($i, $j ) = (  0, -1 );
    
    for ($next[0] = -1; $i < $m; ) {
        # Note that this while() is skipped during the first for() pas
+s.
        while ( $j > -1 &&
                substr( $P, $i, 1 ) ne substr( $P, $j, 1 ) ) {
            $j = $next[ $j ];
        }
        $i++;
        $j++;
        $next[ $i ] =
            substr( $P, $j, 1 ) eq substr( $P, $i, 1 ) ?
                $next[ $j ] : $j;
    }
   return ( $m, @next ); # Length of pattern and prefix function.
}

#######################################
sub knuth_morris_pratt {
    my ( $T, $P ) = @_; # Text and pattern.
    use integer;
    my( $m, @next) = knuth_morris_pratt_next( $P );
    my ( $n, $i, $j ) = ( length($T), 0, 0 );
 
    while ( $i < $n ) {
        while ( $j > -1 && substr( $P, $j, 1 ) ne substr( $T, $i, 1 ) 
+) {
            $j = $next[ $j ];
        }
        $i++;
        $j++;
       
       if($j >= $m){  my $a=$i-$j;
           
       #    $j=$j-1;print "\n";
           
           $j=$next[$j];
           
           for(my $z=0;$z<$m;$z++){
           $loc[$l]=$a;
        $l++;
        $a++;
           }
       
       }
        
    }
    return ; # Mismatch. 
     
}
#################################
[download]

I am new here so apology for any mistake. I am a biologist doing a project in perl.Please Monks help me

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