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Re: match and mismatch

by artist (Parson)
on Nov 14, 2008 at 09:38 UTC ( [id://723605]=note: print w/replies, xml ) Need Help??


in reply to match and mismatch

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]
And here is the output which shows the difference at each position if any. So on '25th' position, you have 'G' in one, and 'T' in the other. 
+ 1 5 

- 2   

- 25 G 
+ 25 T 

- 30 2 
+ 30 4 
- 31 6 
+ 31 0

[download]
--Artist

Replies are listed 'Best First'.
Re^2: match and mismatch
by lima1 (Curate) on Nov 14, 2008 at 17:49 UTC
    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.
[reply]

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