GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Ace::Sequence::GappedAlignment(3) User Contributed Perl Documentation Ace::Sequence::GappedAlignment(3)

Ace::Sequence::GappedAlignment - Gapped alignment object

    # 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);

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.

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.

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.

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

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.

Hey! The above document had some coding errors, which are explained below:
Around line 166:
You forgot a '=back' before '=head1'
2001-11-10 perl v5.32.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.