=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 6.

TAIR7_cdna_20070425 (Arabidopsis CDNA Fasta file, 52MB). 

Bio::Grep v0.10.1. 

=head2 Database Generation

Average over 2 iterations.

  GUUGle         :  11.75 sec
  Agrep/RE       :  24.36 sec
  Vmatch (-pl 3) : 187.65 sec

  
=head2 Mismatches

Query: C<ugacagaagagagugagcac> (revcom)

Average over 20 iterations.

=over

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

  Agrep (Wu-Manber):  0.60 sec
  Vmatch           :  2.81 sec
  RE               :  1.82 sec
  Vmatch (-online) :  4.14 sec
  GUUGle           : 10.13 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           :  0.15 sec
  Agrep (Wu-Manber):  1.09 sec
  Vmatch (-online) :  4.21 sec
  Agrep (TRE)      : 47.01 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Two mismatches:>

  Vmatch           :  0.20 sec
  Agrep (Wu-Manber):  1.44 sec
  Vmatch (-online) :  4.33 sec
  Agrep (TRE)      : 59.17 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Three mismatches:>

  Vmatch           :  0.46 sec
  Agrep (Wu-Manber):  1.93 sec
  Vmatch (-online) :  4.78 sec
  Agrep (TRE)      : 72.56 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Four mismatches:>

  Vmatch           :  1.65 sec
  Agrep (Wu-Manber):  2.29 sec
  Vmatch (-online) :  5.27 sec
  Agrep (TRE)      : 83.50 sec
  GUUGle           :       n/a
  RE               :       n/a

=item B<Five mismatches:>

  Agrep (Wu-Manber):  2.95 sec
  Vmatch           :  6.90 sec
  Vmatch (-online) :  9.00 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  by M. Riester. All rights reserved. 

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
