There is a neat trick for finding difference between similar equal length ASCII strings: xor them together and any non-zero bytes are different. Consider:

use strict;
use warnings;

my $one= "AGCTGATCGAGCTAGTACCCTAGCTC";
my $two= "AGCTGATCGAGCTAGTACCCTATCTC";
my $diff = $one ^ $two;

$diff =~ tr/\0/x/c;

my $start = -1;

while (-1 < ($start = index $diff, 'x', ++$start)) {
    print "Difference at $start\n";
}
[download]

Prints:

Difference at 22
[download]

The tr/// changes non-zero bytes to x. The while loop then uses index to search through the difference string for the x bytes and reports their index (0 based position).

The tr/// changes non-zero bytes to x. The while loop then uses index to search through the difference string for the x bytes and reports their index (0 based position).

I think it might be simpler to use a global regex match for non-nulls and pos. You can just match them for 1-based counting or put them in a look-ahead for 0-based counting. Note that I added another difference in the third characters to check that it was working as I had hoped.

use strict;
use warnings;

my $one  = "AGCTGATCGAGCTAGTACCCTAGCTC";
my $two  = "AGATGATCGAGCTAGTACCCTATCTC";
# Diffs here  ^                   ^

my $diff = $one ^ $two;

my @posns = ();

push @posns, pos $diff while $diff =~ m{[^\0]}g;
print qq{Differences, 1-based counting, at - @posns\n};

@posns = ();

push @posns, pos $diff while $diff =~ m{(?=[^\0])}g;
print qq{Differences, 0-based counting, at - @posns\n};
[download]

The output.

Differences, 1-based counting, at - 3 23
Differences, 0-based counting, at - 2 22
[download]

I hope this is of interest.

Cheers,

JohnGG

i will write the complete problem i am facing. Here is the input file i am using.

sxoght: #query  hit     score   probability     qstart  qend    qorien
+tation    tstart  tend    matches mismatches      gapOpening      gap
+s
@SNPSTER4_104_308EFAAXX:1:1:1694:128
GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT
1 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1694:128     gi|122939163|ref|NM_00
+0165.3|   -10     1.000000        1       36      +       1595    163
+0    35      1   00
Score = -10, P(A|R) = 1.000000
Query:          1 GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT 36
                  |||||||||||||||||||||||||||||| |||||
Sbjct:       1595 GGGATAAGAGAGGTGCATGTTGGTATTTAAAGTAGT 1630

@SNPSTER4_104_308EFAAXX:1:1:1608:94
GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT
14 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1608:94      gi|113412254|ref|XR_01
+8775.1|   0       0.090884        1       36      +       1578    161
+3    36      0   00
Score = 0, P(A|R) = 0.090884
Query:          1 GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT 36
                  ||| |||||||||||||||||||||||||||||| |
Sbjct:       1578 GCATTTTTAAGTTATTAGTTTTTAAAATCAGTACGT 1613
[download]

this is a big file, though the whole file looks like this. What i am trying to do exactly is to grep the header (sxoght) for display in columns and also to display where there is a mismatch in the alignment between query and sbjct. for this input file, the expected results should look like:

>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    36    36    -10    1    1.000000    35    
mismatch : 1625.GA        
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    1    0.090884    36    
mismatch : 1581.GT 1612.TG
[download]

the code which i have written is :

#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file";
while($var=<FILE>){
    $str1=();$str2=();
    if($var=~/^sxoght:/){
        @ar=split(/\s+/,$var);
    print ">$ar[2]\t$ar[8]\t$ar[9]\t$ar[1]\t$ar[5]\t$ar[10]\t$ar[6]\t$
+ar[3]\t$ar[4]\t$ar[11]\n";
    }
    if($var=~/^Query:/){
        $str1=$var;
        $str1=~s/^Query:\s+//g;
        $str1=~s/\d+\s+//g;
        $str1=~s/\s+//g;
    }
    if($var=~/^Sbjct:/){
        $str2=$var;
        $str2=~s/^Sbjct:\s+//g;
        $str2=~s/\d+\s+//g;
        $str2=~s/\s+//g;
    }
    for($i=0;$i<=length($str1);$i++)
    {
    if(substr($str1,$i,1) ne substr($str2,$i,1)){
        print substr($str1,$i,1);
        print substr($str2,$i,1);
        print "$i\n";        
    }
    }
}
[download]

I am not able to use "strict and warning" because using it doesnt allow me to access the scalar variable outside the loop. In my code, i m trying to extract the positions first, so that i will subtract it from the already stored @arr values of beginning and start. I am having problems with the for loop. I know where i am going wrong, but dont know how to correct it. PLEASEEEE HELP !!!

You should only print the output if $str1 and $str2 are both set, and then, clear them so you don't print them again.

The next is very close to your code, but kind of works. You only need to format the output as desired (I don't know where the large numbers come from):

#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file: $!";
while($var=<FILE>){
    if($var=~/^sxoght:/){
        ($str1,$str2)=();
        @ar=split(/\s+/,$var);
        print ">$ar[2]\t$ar[8]\t$ar[9]\t$ar[1]\t$ar[5]\t$ar[10]\t$ar[6
+]\t$ar[3]\t$ar[4]\t$ar[11]\n";
    }
    if($var=~/^Query:/){
        $str1=$var;
        $str1=~s/^Query:\s+//g;
        $str1=~s/\d+\s+//g;
        $str1=~s/\s+//g;
    }
    if($var=~/^Sbjct:/){
        $str2=$var;
        $str2=~s/^Sbjct:\s+//g;
        $str2=~s/\d+\s+//g;
        $str2=~s/\s+//g;
    }
    if(defined $str1 and defined $str2) {
        for($i=0;$i<=length($str1);$i++)
        {
            if(substr($str1,$i,1) ne substr($str2,$i,1)){
                # this is not in the desired format, yet
                print substr($str1,$i,1);
                print substr($str2,$i,1);
                print "$i\n";
            }
        }
        ($str1,$str2)=();
    }
}
[download]

For the format, I propose to store the results in an array, and print "mismatch:" only if the array isn't empty at the end.

        my @mismatch;
        for($i=0;$i<=length($str1);$i++)
        {
            if(substr($str1,$i,1) ne substr($str2,$i,1)){
                push @mismatch, "$i." . substr($str1,$i,1) . substr($s
+tr2,$i,1);
            }
        }
        if(@mismatch) {
            print "mismatch: @mismatch\n";
        }
[download]

After that modification, the output I get for this file is

>hit    tstart    tend    #query    qstart    matches    qend    score
+    probability    mismatches
>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    35    36    -10    1.000000    1
mismatch: 30.GA
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    0.090884    0
mismatch: 3.GT 34.TG
[download]

p.s. There's a possible speed improvement if you XOR (^) the two strings, you'll get a string of null bytes for where they are the same and non null where they are not:

        my $xor = $str1 ^ $str2;
        while($xor =~ /[^\0]/g) {
            my $i = pos($xor) - 1;  # or: $-[0]
            push @mismatch, "$i." . substr($str1,$i,1) . substr($str2,
+$i,1);
        }
[download]

but u did not define here @var and @ar

my $one = "1  AGCTGATCGAGCTAGTACCCTAGCTC 26";
my $two = "15 AGCTGATCGAGCTAGTACCCTATCTC 40";

my @one = split '\s+', $one;
my @two = split '\s+', $two;

if ($one[1] ne $two[1]) {
    my $matchlen = ($one[1] ^ $two[1]) =~ /\A(\0+)/ 
                   ? length($1) 
                   : 0;
    print "Mismatch at ",
       $one[0] + $matchlen, ' and ', 
       $two[0] + $matchlen, "\n";
}
else  {
    print "full match\n";
}
[download]

see Bitwise-String-Operators

use Algorithm::Diff qw(diff sdiff LCS traverse_sequences);            
+          
my @seq1= split //,"1  AGCTGATCGAGCTAGTACCCTAGCTC 26";
my @seq2 =split //,"15 AGCTGATCGAGCTAGTACCCTATCTC 40";

my  @diffs = diff( \@seq1, \@seq2 );
foreach (@diffs) {
    foreach (@{$_}) {
       print join " " => @{$_},"\n";        
    }
    print "\n";
    
}
[download]

+ 1 5 

- 2   

- 25 G 
+ 25 T 

- 30 2 
+ 30 4 
- 31 6 
+ 31 0
[download]

Just for the sake of completeness: The runtime here is N^2. The identifcation of mismatches is obviously possible in N (see solutions above). But this solution is much more powerful and can identify insertions and deletions as well.

sure, i will write the complete problem i am facing. Here is the input file i am using.

sxoght: #query  hit     score   probability     qstart  qend    qorien
+tation    tstart  tend    matches mismatches      gapOpening      gap
+s
@SNPSTER4_104_308EFAAXX:1:1:1694:128
GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT
1 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1694:128     gi|122939163|ref|NM_00
+0165.3|   -10     1.000000        1       36      +       1595    163
+0    35      1   00
Score = -10, P(A|R) = 1.000000
Query:          1 GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT 36
                  |||||||||||||||||||||||||||||| |||||
Sbjct:       1595 GGGATAAGAGAGGTGCATGTTGGTATTTAAAGTAGT 1630

@SNPSTER4_104_308EFAAXX:1:1:1608:94
GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT
14 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1608:94      gi|113412254|ref|XR_01
+8775.1|   0       0.090884        1       36      +       1578    161
+3    36      0   00
Score = 0, P(A|R) = 0.090884
Query:          1 GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT 36
                  ||| |||||||||||||||||||||||||||||| |
Sbjct:       1578 GCATTTTTAAGTTATTAGTTTTTAAAATCAGTACGT 1613
[download]

this is a big file, though the whole file looks like this. What i am trying to do exactly is to grep the header (sxoght) for display in columns and also to display where there is a mismatch in the alignment between query and sbjct. for this input file, the expected results should look like:

>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    36    36    -10    1    1.000000    35    
mismatch : 1625.GA        
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    1    0.090884    36    
mismatch : 1581.GT 1612.TG
[download]

the code which i have written is :

#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file";
while($var=<FILE>){
    $str1=();$str2=();
    if($var=~/^sxoght:/){
        @ar=split(/\s+/,$var);
    print ">$ar[2]\t$ar[8]\t$ar[9]\t$ar[1]\t$ar[5]\t$ar[10]\t$ar[6]\t$
+ar[3]\t$ar[4]\t$ar[11]\n";
    }
    if($var=~/^Query:/){
        $str1=$var;
        $str1=~s/^Query:\s+//g;
        $str1=~s/\d+\s+//g;
        $str1=~s/\s+//g;
    }
    if($var=~/^Sbjct:/){
        $str2=$var;
        $str2=~s/^Sbjct:\s+//g;
        $str2=~s/\d+\s+//g;
        $str2=~s/\s+//g;
    }
    for($i=0;$i<=length($str1);$i++)
    {
    if(substr($str1,$i,1) ne substr($str2,$i,1)){
        print substr($str1,$i,1);
        print substr($str2,$i,1);
        print "$i\n";        
    }
    }
}
[download]

I am not able to use "strict and warning" because using it doesnt allow me to access the scalar variable outside the loop. In my code, i m trying to extract the positions first, so that i will subtract it from the already stored @arr values of beginning and start. I am having problems with the for loop. I know where i am going wrong, but dont know how to correct it. PLEASEEEE HELP !!!

I don't believe this is the complete program, because I don't see where your variables are being defined. If the my statements are inside a loop, by definition you can't see the variable outside the loop (and use strict; use warnings; are correcly telling you so.)

So, please show the program you are trying to run, and we'll try this again.