- AUTHOR - Jason Stajich
Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
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);
Calculate pairwise statistics.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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>
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>
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>
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]