Ace::Sequence::Homol

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 <[email protected]> with extensive help from Jean Thierry-Mieg <[email protected]> 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.