Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Align::PairwiseStUsertContributed Perl DBio::Align::PairwiseStatistics(3)

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]

perl v5.24.1			  2017-07-08 Bio::Align::PairwiseStatistics(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Align::PairwiseStatistics&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

home | help