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Bio::Align::ProteinStatistics.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
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 = new Bio::AlignIO(-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
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AUTHOR - Jason Stajich
Email jason-at-bioperl.orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : my $obj = new Bio::Align::ProteinStatistics(); 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)
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre