| Bio::Align::PairwiseStatistics(3pm) | User Contributed Perl Documentation | Bio::Align::PairwiseStatistics(3pm) |
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]
| 2020-10-28 | perl v5.30.3 |