GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::ALIGN::PROTEINSTATISTICS (3)

.ds Aq ’

NAME

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

CONTENTS

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)



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::ALIGN::PROTEINSTATISTICS (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.