---
name: "Ace::Sequence::GappedAlignment"
section: "3pm"
platform: "linux"
package: "libace-perl"
version: "1.92-12+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Ace::Sequence::GappedAlignment"
---

# Ace::Sequence::GappedAlignment(3pm)

Gapped alignment object

## 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'