1Ace::Sequence::Homol(3)User Contributed Perl DocumentatioAnce::Sequence::Homol(3)
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NAME

6       Ace::Sequence::Homol - Temporary Sequence Homology Class
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SYNOPSIS

9           # Get all similarity features from an Ace::Sequence
10           @homol = $seq->features('Similarity');
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12           # sort by score
13           @sorted = sort { $a->score <=> $b->score } @homol;
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15           # the last one has the highest score
16           $best = $sorted[$#sorted];
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18           # fetch its associated Ace::Sequence::Homol
19           $homol = $best->target;
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21           # print out the sequence name, DNA, start and end
22           print $homol->name,' ',$homol->start,'-',$homol->end,"\n";
23           print $homol->asDNA;
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DESCRIPTION

26       Ace::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence)
27       which is specialized for returning information about a DNA or protein
28       homology.  This is a temporary placeholder for a more sophisticated
29       homology class which will include support for alignments.
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OBJECT CREATION

32       You will not ordinarily create an Ace::Sequence::Homol object directly.
33       Instead, objects will be created in response to an info() or group()
34       method call on a similarity feature in an Ace::Sequence::Feature
35       object.  If you wish to create an Ace::Sequence::Homol object directly,
36       please consult the source code for the new() method.
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OBJECT METHODS

39       Most methods are inherited from Ace::Object.  The following methods are
40       also supported:
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42       start()
43             $start = $homol->start;
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45           Returns the start of the area that is similar to the
46           Ace::Sequence::Feature from which his homology was derived.
47           Coordinates are relative to the target homology.
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49       end()
50             $end = $homol->end;
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52           Returns the end of the area that is similar to the
53           Ace::Sequence::Feature from which his homology was derived.
54           Coordinates are relative to the target homology.
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56       asString()
57             $label = $homol->asString;
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59           Returns a human-readable identifier describing the nature of the
60           feature.  The format is:
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62            $name/$start-$end
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64           for example:
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66            HUMGEN13/1-67
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68           This method is also called automatically when the object is treated
69           in a string context.
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SEE ALSO

72       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList,
73       Ace::Sequence::Feature, GFF
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AUTHOR

76       Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-
77       Mieg <mieg@kaa.crbm.cnrs-mop.fr>
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79       Copyright (c) 1999, Lincoln D. Stein
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81       This library is free software; you can redistribute it and/or modify it
82       under the same terms as Perl itself.  See DISCLAIMER.txt for
83       disclaimers of warranty.
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87perl v5.30.0                      2019-07-26           Ace::Sequence::Homol(3)
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