Ace::Sequence::Homol - Temporary Sequence Homology Class
# Get all similarity features from an Ace::Sequence @homol = $seq->features('Similarity'); # sort by score @sorted = sort { $a->score <=> $b->score } @homol; # the last one has the highest score $best = $sorted[$#sorted]; # fetch its associated Ace::Sequence::Homol $homol = $best->target; # print out the sequence name, DNA, start and end print $homol->name,' ',$homol->start,'-',$homol->end,"\n"; print $homol->asDNA;
Ace::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence) which is specialized for returning information about a DNA or protein homology. This is a temporary placeholder for a more sophisticated homology class which will include support for alignments.
You will not ordinarily create an Ace::Sequence::Homol object directly. Instead, objects will be created in response to an info() or group() method call on a similarity feature in an Ace::Sequence::Feature object. If you wish to create an Ace::Sequence::Homol object directly, please consult the source code for the new() method.
Most methods are inherited from Ace::Object. The following methods are also supported:
$start = $homol->start;
Returns the start of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are relative to the target homology.
$end = $homol->end;
Returns the end of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are relative to the target homology.
$label = $homol->asString;
Returns a human-readable identifier describing the nature of the feature. The format is:
$name/$start-$end
for example:
HUMGEN13/1-67
This method is also called automatically when the object is treated in a string context.
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList, Ace::Sequence::Feature, GFF
Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
To install Ace, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Ace
CPAN shell
perl -MCPAN -e shell install Ace
For more information on module installation, please visit the detailed CPAN module installation guide.