/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Align::ProteinStatistics

NAME

Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)

SYNOPSIS

  use Bio::Align::ProteinStatistics;
  use Bio::AlignIO;
  my $in = Bio::AlignIO->new(-format => 'fasta',
			    -file   => 'pep-104.fasaln');
  my $aln = $in->next_aln;

  my $pepstats = Bio::Align::ProteinStatistics->new();
  $kimura = $protstats->distance(-align => $aln,
			         -method => 'Kimura');
  print $kimura->print_matrix;

DESCRIPTION

This object is for generating various statistics from a protein alignment. Mostly it is where pairwise protein distances can be calculated.

REFERENCES

D_Kimura - Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, Cambridge.

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.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = Bio::Align::ProteinStatistics->new();
Function: Builds a new Bio::Align::ProteinStatistics object 
Returns : an instance of Bio::Align::ProteinStatistics
Args    :

distance

 Title   : distance
 Usage   : my $distance_mat = $stats->distance(-align  => $aln, 
		 			       -method => $method);
 Function: Calculates a distance matrix for all pairwise distances of
           sequences in an alignment.
 Returns : L<Bio::Matrix::PhylipDist> object
 Args    : -align  => Bio::Align::AlignI object
           -method => String specifying specific distance method 
                      (implementing class may assume a default)

available_distance_methods

Title   : available_distance_methods
Usage   : my @methods = $stats->available_distance_methods();
Function: Enumerates the possible distance methods
Returns : Array of strings
Args    : none

D - distance methods

D_Kimura

Title   : D_Kimura
Usage   : my $matrix = $pepstats->D_Kimura($aln);
Function: Calculate Kimura protein distance (Kimura 1983) which 
          approximates PAM distance
          D = -ln ( 1 - p - 0.2 * p^2 )
Returns : L<Bio::Matrix::PhylipDist>
Args    : L<Bio::Align::AlignI>

Data Methods

pairwise_stats

Title   : pairwise_stats
Usage   : $obj->pairwise_stats($newval)
Function: 
Returns : value of pairwise_stats
Args    : newvalue (optional)