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ACE::SEQUENCE::GAPPEDALIGNMENT(3PM) - Linux man page online | Library functions

Gapped alignment object.

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2017-11-24
Ace::Sequence::GappedAlignment(User Contributed Perl DocumentaAce::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 <@cshl.org> with extensive help from Jean Thierry-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 v5.26.1 2017-11-24 Ace::Sequence::GappedAlignment(3pm)
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