1Ace::Sequence::Homol(3)User Contributed Perl DocumentatioAnce::Sequence::Homol(3)
2
3
4

NAME

6       Ace::Sequence::Homol - Temporary Sequence Homology Class
7

SYNOPSIS

9           # Get all similarity features from an Ace::Sequence
10           @homol = $seq->features('Similarity');
11
12           # sort by score
13           @sorted = sort { $a->score <=> $b->score } @homol;
14
15           # the last one has the highest score
16           $best = $sorted[$#sorted];
17
18           # fetch its associated Ace::Sequence::Homol
19           $homol = $best->target;
20
21           # print out the sequence name, DNA, start and end
22           print $homol->name,' ',$homol->start,'-',$homol->end,"\n";
23           print $homol->asDNA;
24

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.
30

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.
37

OBJECT METHODS

39       Most methods are inherited from Ace::Object.  The following methods are
40       also supported:
41
42       start()
43             $start = $homol->start;
44
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.
48
49       end()
50             $end = $homol->end;
51
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.
55
56       asString()
57             $label = $homol->asString;
58
59           Returns a human-readable identifier describing the nature of the
60           feature.  The format is:
61
62            $name/$start-$end
63
64           for example:
65
66            HUMGEN13/1-67
67
68           This method is also called automatically when the object is treated
69           in a string context.
70

SEE ALSO

72       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList,
73       Ace::Sequence::Feature, GFF
74

AUTHOR

76       Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-
77       Mieg <mieg@kaa.crbm.cnrs-mop.fr>
78
79       Copyright (c) 1999, Lincoln D. Stein
80
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.
84
85
86
87perl v5.38.0                      2023-07-20           Ace::Sequence::Homol(3)
Impressum