Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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);
            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]