=head1 NAME

Bio::Grep::Benchmarks - Bio::Grep Benchmarks

=head1 DESCRIPTION

A collection of quick and dirty benchmarks. 

=head1 BENCHMARKS

2 x Intel(R) Xeon(TM) CPU 2.40GHz, 1GB RAM. Fedora Core 8.

TAIR8_cdna_20080412 (Arabidopsis CDNA Fasta file, 63MB). 

Bio::Grep 0.10.5. 

=head2 Database Generation

Average over 2 iterations.

  GUUGle         : 6.29 sec
  Agrep/RE       : 18.50 sec
  Vmatch (-pl 3) : 208.14 sec

  
=head2 Mismatches

Query: C<ugacagaagagagugagcac> (revcom)

Average over 20 iterations.

=over

=item B<No mismatches (exact matching):>

  Agrep (Wu-Manber):  0.62 sec
  Vmatch           :  2.27 sec
  RE               :  2.17 sec
  Vmatch (-online) :  5.09 sec
  GUUGle           : 16.21 sec
  Agrep (TRE)      : 15.96 sec

Note that C<Vmatch> needs one slow run to load the suffix arrays in memory
(Values are the average over 20 iterations). Also note that GUUGle
allows GU mismatches.

=item B<One mismatch:>

  Vmatch           :  0.08 sec
  Agrep (Wu-Manber):  1.31 sec
  Vmatch (-online) :  5.53 sec
  Agrep (TRE)      : 47.01 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Two mismatches:>

  Vmatch           :  0.23 sec
  Agrep (Wu-Manber):  1.66 sec
  Vmatch (-online) :  6.01 sec
  Agrep (TRE)      : 59.17 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Three mismatches:>

  Vmatch           :  0.54 sec
  Agrep (Wu-Manber):  2.13 sec
  Vmatch (-online) :  6.34 sec
  Agrep (TRE)      : 72.56 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Four mismatches:>

  Vmatch           :  1.77 sec
  Agrep (Wu-Manber):  2.49 sec
  Vmatch (-online) :  7.22 sec
  Agrep (TRE)      : 83.50 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Five mismatches:>

  Agrep (Wu-Manber):  3.32 sec
  Vmatch           :  7.49 sec
  Vmatch (-online) : 11.68 sec
  Agrep (TRE)      : 96.16 sec
  GUUGle           :       n/a
  RE               :       n/a

=back

=head1 FEEDBACK

The script that generated these benchmarks is available in the I<examples>
directory of this distribution. 

Please report any bugs, feature requests and benchmarks to
C<bug-bio-grep@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>. 

=head1 AUTHOR

Markus Riester, E<lt>mriester@gmx.deE<gt>


=head1 LICENCE AND COPYRIGHT

Copyright (C) 2007-2008  by M. Riester. 

This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.

=cut

# vim: ft=perl sw=4 ts=4 expandtab
