---
name: "Ace::Sequence::Homol"
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::Homol"
---

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

Temporary Sequence Homology Class

## 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 \<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.