Bio::Align::PairwiseStatistics.3pm

Langue: en

Autres versions - même langue

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

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

SYNOPSIS

   use strict;
   my $stats = Bio::Align::DNAStatistics->new();
 
   # get alignment object of two sequences somehow
   my $pwaln;
   print $stats->number_of_comparable_bases($pwaln);

DESCRIPTION

Calculate pairwise statistics.

FEEDBACK


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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
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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:

   http://bugzilla.open-bio.org/

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>