comment on

I have a large set (100000+) of short DNA reads 20 characters long. I need to compares all reads against each other and pull out those that vary by just 1 position. Heres the script I came up with.

$| = 1;
my $compare_count = 0;
for (my $i = 0; $i < @kmers; $i++ ) {
    for (my $j = $i + 1; $j < @kmers; $j++ ) {
        print "\rComparing sequence $i to $j";
        my @result = PCCompare::dissimilarity($kmers[$i], $kmers[$j], 
+1);
        if ($result[0] == 1) {
            print "\rMatch found: $kmers[$i], $kmers[$j]\n";
            push @variant_kmers, ($kmers[$i], $kmers[$j]);
        }
        $compare_count++;
    }
}
print "\rFinished: $compare_count comparisions made.\n";
[download]

The problem is that this loop runs very very slow. It takes on the orders of days to process 100000 sequences. Is there a way to make the process faster?

In reply to Comparing a large set of DNA sequences by shamshersingh

Are you posting in the right place? Check out Where do I post X? to know for sure.
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
Want more info? How to link or How to display code and escape characters are good places to start.


Perl Monk, Perl Meditation
	PerlMonks