Ace::S...nscript(3pm)

🧬 NAME 🧬

okay bestie so this is Ace::Sequence::Transcript — no wait, it's literally described as a Simple "Gene" Object 💅 iykyk, the naming is giving chaos but we move. It's Ace::Sequence::Transcript up top and Ace::Sequence::Gene everywhere else, and that's just how it is, no cap.

It's from the User Contributed Perl Documentation crew ✨

---

✨ SYNOPSIS ✨

ok so real quick, here's the vibe of how you actually use this thing:

    # open database connection and get an Ace::Object sequence
    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 transcripts
    @genes = $seq->transcripts;

    # get the exons from the first one
    @exons = $genes[0]->exons;

    # get the introns
    @introns = $genes[0]->introns

    # get the CDSs (NOT IMPLEMENTED YET!)
    @cds = $genes[0]->cds;

like, look at her go 🫶 she's got the whole gene anatomy mapped out — exons, introns, and someday (not today!!) the CDSs.

---

🌸 DESCRIPTION 🌸

Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. She inherits every single method Ace::Sequence::Feature has — all of them, no stealing — but then she also adds the ability to retrieve the annotated introns and exons of the gene. That's her whole specialty, that's her thing, that's her main character energy 👑

---

🎀 OBJECT CREATION 🎀

okay listen, you will not ordinarily create an Ace::Sequence::Gene object directly. Like, don't do that, bestie. That's not the move.

Instead, these objects get created for you in response to a transcripts() call to an Ace::Sequence object. She just shows up. Unbothered. Perfect. 💅

---

💖 OBJECT METHODS 💖

Most methods are inherited from Ace::Sequence::Feature — she's sharing the whole closet. But the following methods are also supported:

• exons() — gives you the annotated exons.

      @exons = $gene->exons;

Return a list of Ace::Sequence::Feature objects corresponding to annotated exons. cute little exon features, all lined up 🧚

• introns() — gives you the annotated introns.

      @introns = $gene->introns;

Return a list of Ace::Sequence::Feature objects corresponding to annotated introns. yes babes, the in-between bits get love too 💜

• cds() — gives you... well, supposedly the coding sequence.

      @cds = $gene->cds;

Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED. 😭 so like, don't rely on it, she's still in her beta era.

• relative() — the coordinate system toggle, she's the vibe check for your numbers.

      $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. ✨

note the "usually" — the original says usually, and we respect the original 💯

---

🔥 SEE ALSO 🔥

go read these next bestie, they're all linked up:

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> 🫶 iconic collab fr 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.

---

ok so that's the whole thing, you're fully caught up bestie 🌈 this little gem came to you via perl v5.42.3 on 2026-08-19, and that's the tea 🍓 go forth and annotate those exons 💖💅✨