NAME

Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments

SYNOPSIS

use strict;
my $stats = Bio::Align::PairwiseStatistics->new();

# get alignment object of two sequences somehow
my $pwaln;
print $stats->number_of_comparable_bases($pwaln);
my $score = $stats->score_nuc($pwaln);

DESCRIPTION

Calculate pairwise statistics.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

number_of_comparable_bases

Title   : number_of_comparable_bases
Usage   : my $bases = $stat->number_of_comparable_bases($aln);
Function: Returns the count of the number of bases that can be
          compared (L) in this alignment ( length - gaps)
Returns : integer
Args    : L<Bio::Align::AlignI>

number_of_differences

Title   : number_of_differences
Usage   : my $nd = $stat->number_of_distances($aln);
Function: Returns the number of differences between two sequences
Returns : integer
Args    : L<Bio::Align::AlignI>

number_of_gaps

Title   : number_of_gaps
Usage   : my $nd = $stat->number_of_gaps($aln);
Function: Returns the number of gapped positions among sequences in alignment
Returns : integer
Args    : L<Bio::Align::AlignI>

score_nuc

Title   : score_nuc
Usage   : my $score = $stat->score_nuc($aln);
            or
          my $score = $stat->score_nuc(
            -aln =>$aln,
            -match    => 1,
            -mismatch => -1,
            -gap_open => -1,
            -gap_ext  => -1
          );
Function: Calculate the score of an alignment of 2 nucleic acid sequences. The
          scoring parameters can be specified. Otherwise the blastn default
          parameters are used: match = 2, mismatch = -3, gap opening = -5, gap
          extension = -2
Returns : alignment score (number)
Args    : L<Bio::Align::AlignI>
          match score [optional]
          mismatch score [optional]
          gap opening score [optional]
          gap extension score [optional]