Bio::Align::ProteinStatistics.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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

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)