ace::sequence::homol(3pm) [debian man page]

Ace::Sequence::Homol(3pm)				User Contributed Perl Documentation				 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,"
";
	   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 v5.14.2							    2001-09-17						 Ace::Sequence::Homol(3pm)

Ace::Sequence::GappedAlignment(3pm)			User Contributed Perl Documentation		       Ace::Sequence::GappedAlignment(3pm)

NAME

       Ace::Sequence::GappedAlignment - Gapped alignment object

SYNOPSIS

	   # open database connection and get an Ace::Sequence object
	   use Ace::Sequence;

	   # get a megabase from the middle of chromosome I
	   $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
				     -db     => $db,
				     -offset => 3_000_000,
				     -length => 1_000_000);

	   # get all the gapped alignments
	   @alignments = $seq->alignments('EST_GENOME');

	   # get the aligned segments from the first one
	   @segs = $alignments[0]->segments;

	   # get the position of the first aligned segment on the
	   # source sequence:
	   ($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);

	   # get the target position for the first aligned segment
	   ($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);

DESCRIPTION

       Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature.	It inherits all the methods of Ace::Sequence::Feature, but adds
       the ability to retrieve the positions of the aligned segments.  Each segment is an Ace::Sequence::Feature, from which you can retrieve the
       source and target coordinates.

OBJECT CREATION

       You will not ordinarily create an Ace::Sequence::GappedAlignment object directly.  Instead, objects will be created in response to a
       alignments() call to an Ace::Sequence object.

OBJECT METHODS

       Most methods are inherited from Ace::Sequence::Feature.	The following methods are also supported:

       segments()
	     @segments = $gene->segments;

	   Return a list of Ace::Sequence::Feature objects corresponding to similar segments.

       relative()
	     $relative = $gene->relative;
	     $gene->relative(1);

	   This turns on and off relative coordinates.	By default, the exons and intron features will be returned in the coordinate system used
	   by the gene.  If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene.  The first
	   exon will (usually) be 1.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF

AUTHOR

       Lincoln Stein <lstein@cshl.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.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 166:
	   You forgot a '=back' before '=head1'

perl v5.14.2							    2001-11-10				       Ace::Sequence::GappedAlignment(3pm)