yeah dudes, you are rite, but i ve already done that, i mean, i have used index for string matching, but this is a try to find string matching in a different method, am jus giving a try to do it. this is what i have done so far. 
#!/usr/bin/perl 
#ENTERING A MOTIF TO BE SEARCHED FROM USER INPUT
print "Enter a pattern to be searched:";
$seq =<STDIN>;
chomp($seq);
@seqss = split ('',$seq);
$m=scalar @seqss;
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[$m-1];
#ASSIGNING KEY VALUES TO MOTIFS
my @unique = ();
my %seen   = ();
@pats=reverse @seqss;
foreach my $elem ( @pats )
{
next if $seen{ $elem }++;
push @uni, $elem;
@unique= reverse @uni;
}
$cc=1;
foreach (@uni)
{
    $count{$_} = $cc;
    $cc++;
}
$zen = $m+1;
for(my $i=0;$i<scalar @unique;$i++)
{
$mcut=scalar @unique;
$m=$mcut-$i;
%num=("$unique[$i]"=>"$m");
while (($key1, $val1) = each(%num))
{
push(@key,$key1);
push(@val,$val1);
}
}
#OPENING A DATABASE (A TEXT FILE WHERE STRINGS OF ALPHABETS SAVED)
open (PIR,'/home/httpd/heidi/fasta/pir/heidi_pir/pirdb.txt');
$count=0;
while (<PIR>)
{
    if (/^ENTRY/)
        {$entry = $_;}
    elsif (/^>gi/)
        {$gi = $_;}
    elsif(/^TITLE/)
        {$title = (s/                   /\n\t\t /g,$_);}
    elsif(/^ORGANISM/)
        {$org = (s/                   /\n\t\t /g,$_);}
    elsif(/^ACCESSIONS/)
        {$acc = $_;}
    else
    {
        @array2 = $_;
    }
    #what i need is only this from the database (ie., the string where
+ i have to match the motif or pattern)
    if (defined $array2[0])
    {
        @onlyseq = split('',$array2[0]);    
    }
    @array2=();
    #ASSIGNING KEY VALUES FOR THE STRING INCLUDING MOTIFS(VALUES)
    foreach $_(@onlyseq)
    {
        if($count{$_} != $zen)
        {
            if (defined $count{$_})
            {
                push(@a,$count{$_});
                push(@b,$_);
                #print @a;
                #print @b;
            }
            else
            {
                push(@a,$zen);
                push(@b,$_);
                #print @a;
                #print @b;
            }
        }
                
    }
    #SEARCHING FOR MOTIFS IN THE STRING<< THIS IS WHERE I AM STUCK WIT
+H>>
        $m=scalar @seqss;
        for(my $i=$m;$i<=scalar @a;$i++)
        {
        #COMPARING THE LAST AND THE FIRST CHARACTER
            if(($lastch eq $b[$i]) && ($firstch eq $b[$i-($m-1)]))
            {
            #I WANT TO COMPARE THE INBETWEEN CHARACTERS HERE ITSELF.((
+( WHERE I NEED YOUR HELP)))
                #for(my $j=($i-($m-1));$j<=$i;$j++)
                #{
                #    push(@fnum,$a[$j]);
                #    push(@flet,$b[$j]);
                #}
                #$t=$i+1;
                #$i=$t+$i-1;
                
            }
        }
        $m=scalar @seqss;
        while (@flet) 
        { 
            push(@words, join('', splice(@flet, 0, $m))); 
        }
        #print "@words\n";
        foreach (@words)
        {
        next unless $_ =~ /$seq/; 
        print("$_\n");
        $count++;
        }    
        @onlyseq=();
        @a=();
        @b=();
        @flet=();
        @fnum=();
        @words=();
}
print "\nThe number of patterns found in PIR database : $count\n";

[download]
I bet you wont understand half of wat i have done, thats because i havent explained u the whole algorithm.so just see near the comment #SEARCHING FOR MOTIFS IN THE STRING<< THIS IS WHERE I AM STUCK WITH>> if possible , do suggest a solution. my database file looks like this: 
ENTRY            CCHU       #type complete
TITLE            cytochrome c [validated] - human
ORGANISM         #formal_name Homo sapiens #common_name man
ACCESSIONS       A31764; A05676; I55192; A00001
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLE
+NPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCCZ       #type complete
TITLE            cytochrome c - chimpanzee (tentative sequence)
ORGANISM         #formal_name Pan troglodytes #common_name chimpanzee
ACCESSIONS       A00002
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLEN
+PKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCMQR      #type complete
TITLE            cytochrome c - rhesus macaque (tentative sequence)
ORGANISM         #formal_name Macaca mulatta #common_name rhesus macaq
+ue
ACCESSIONS       A00003
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGITWGEDTLMEYLEN
+PKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCMKP      #type complete
TITLE            cytochrome c - spider monkey
ORGANISM         #formal_name Ateles sp. #common_name spider monkey
ACCESSIONS       A00004
GDVFKGKRIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQASGFTYTEANKNKGIIWGEDTLMEYLEN
+PKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE

[download]

Edited by planetscape - added readmore tags

( keep:2 edit:21 reap:4 )

In reply to here is my program for string matching in a database (Was: Re: doubt in string matching.) by heidi
in thread doubt in string matching. by heidi

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