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Ace::Sequence::Homol(3User Contributed Perl DocumentatiAce::Sequence::Homol(3)

NAME
       Ace::Sequence::Homol - Temporary Sequence Homology Class

SYNOPSIS
	   # 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;

DESCRIPTION
       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.

OBJECT CREATION
       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.

OBJECT METHODS
       Most methods are inherited from Ace::Object.  The following methods are
       also supported:

       start()
	     $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()
	     $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.

       asString()
	     $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.

SEE ALSO
       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList,
       Ace::Sequence::Feature, GFF

AUTHOR
       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.

perl v5.14.1			  2001-09-17	       Ace::Sequence::Homol(3)
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