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Bio::ProteinFeatures - Deriving features of amino acid sequences |
Bio::ProteinFeatures - Deriving features of amino acid sequences
use Bio::ProteinFeatures;
$pf = new Bio::ProteinFeatures;
$pf->sequence($sequence_string);
# you may use Data::Dumper to see the result. use Data::Dumper; print Dumper $pf->features();
This module applies several statistical methods on amino acid sequences for deriving various useful features for identifying sequences and they may be used to measure similarities between sequences. You may also use this module to do coarse matching before doing Blast.
You can set the sequence on invoking the constructor.
$pf = new Bio::ProteinFeatures(sequence => $sequence_string);
Or set it using the next method.
Set or get the sequence string
# set the sequence
$pf->sequence($sequence);
# return the sequence
$pf->sequence();
The features this module deals with are listed below.
Amino acids are grouped into three categories: polar, neutral, and hydrophobic. The methods calculates the compositions of the three groups of amino acids.
Characterizes the percent frequency with which group A is followed by group B or B is followed by A.
Sequences are cut into 5 sections. It calculates the accumulative probabilities of a certain group within a section.
Calculates per-se probability of each amino acid.
summation prob(i**2) for each i of amino acids.
summation -prob(i)*log(prob(i)) for each i of amino acids.
Calculates the difference of the numbers of two neighboring amino acids.
Probabilities of amino acid bigrams.
Counts the average number of characters between two amino acids of the same group.
xern <xern@cpan.org>
This module is free software; you can redistribute it or modify it under the same terms as Perl itself.
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Bio::ProteinFeatures - Deriving features of amino acid sequences |