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Ace::Sequence::Homol.3pm

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.