please try to update it and add tags like  <p>,<c> ...

see Markup in the Monastery

UPDATE: since you're a beginner

-----------------

I wanna match array element patterns($pats[$i]) with the row sequence($str). Also find the overlapping region location in the sequence($str). Please help me. But my loop is not work properly.

Thanks.

INPUT FILES:

seq.txt >seq1 AAAAAA >seq2 TTTTT

pat.txt seq1 AAAAA TTTTT GGGGG

I want following output: Patterns sequence name start end length of seq. AAAAA seq1 1 5 6 AAAAA seq1 2 6 6 TTTTT seq2 1 5 5

not found GGGGG

I wrote following PERL script:

#!/usr/bin/perl-w                                                     
+                      
#  perl program to find motif in text file eith its positions.        
+    
 
use strict;
use Bio::SeqIO;
 
open(my $outfile, ">", "Motif_Result.txt");
 
my $file = 'seq.txt';
 
 
print {$outfile}"\t\t\t\t\t Positions\n";
print {$outfile}"\tPattern Name\tSequence Name\tStart\tEnd\tLength of 
+Sequence\n\n";
 
 
my $patternseq= 'pat.txt';
open(FIH, $patternseq);
 
my $in;
my %patsmap;      my @residue;   my @pats;      my $seqcount = 0;
while ($in=<FIH>)
{
         chomp($in);
         my @pats=split " ",$in;
         my $residue=shift@pats;
         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn}=@residue;
         }
 
        print "Patterns\t"; print "@pats";             print "\n";
        my $length = @pats;
        print "Total Patterns are: $length"; print "\n";
 
 
my $seqobj;
my $in = Bio::SeqIO->new(-format => 'fasta',
                         -file   => $file);
 
my $motif_count = 0;
 
 
 
   while ( my $seq = $in->next_seq)
        {
        $seqcount++;                  # count the number of sequences
        my $head = $seq->display_id();
        my $str = $seq->seq;          # get the sequence as a strin
+g
        $str =~ s/\*//g;              # remove all '*' from sequence
 
my $i;
for ($i=0; $i<=$length; $i++) {
             while ( $str =~ m/(?=$pats<a href="?node=%24i">$i</a>)/ig
+)
                 {
                 my @l = split('', $str);
                 my $length=@l;
         print {$outfile}"\t"; print {$outfile}$pats<a href="?node=%24
+i">$i</a>; 
         printf {$outfile}"\t\t$head\t\t%d", pos($str)+1;
         printf {$outfile}"\t%d", pos($str)+5;
         print {$outfile}"\t";  print {$outfile}$length; print {$outfi
+le}"\n";
                
                 }
        }
 
}
 
print {$outfile}"\n\tTotal Sequences in file name $file\t:$seqcount\n"
+;
 
exit;
     }
[download]

---------------

#!/usr/bin/perl-w
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You need a space between the program name and any switches you need to pass to the program.    Better to just use the warnings pragma:

#!/usr/bin/perl
use warnings;
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open(my $outfile, ">", "Motif_Result.txt");

...

open(FIH, $patternseq);
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You should always verify that the file opened correctly:

open my $outfile, '>', 'Motif_Result.txt' or die "Cannot open 'Motif_R
+esult.txt' $!";

...

open FIH, '<', $patternseq or die "Cannot open '$patternseq' $!";
[download]

my $in;

while ($in=<FIH>)
{
         chomp($in);
         my @pats=split " ",$in;
         my $residue=shift@pats;
[download]

That could more simply be written as:

while ( <FIH> )
{
         my ( $residue, @pats ) = split;
[download]

         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn}=@residue;
         }
[download]

You don't put any values into @residue so that is the same as saying:

         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn} = 0;
         }
[download]

Perhaps you meant to use $residue instead of @residue?

        print "Patterns\t"; print "@pats";             print "\n";
        my $length = @pats;
        print "Total Patterns are: $length"; print "\n";
[download]

Instead of five separate prints you just need one:

        print "Patterns\t@pats\nTotal Patterns are: ", scalar @pats, "
+\n";
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                 my @l = split('', $str);
                 my $length=@l;
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That is usually written as:

                 my $length = length $str;
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exit;
     }
[download]

You exit the program at the bottom of the loop so you only ever read one line from your 'pat.txt' file.

Also see BioPerl.