> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# Borzoi Track Activity

> Score DNA target activity on selected Borzoi output tracks.

<div class="page-hero">
  <img class="page-hero-banner" src="https://proto-bio.github.io/proto-assets/images/constraint/borzoi-track-activity/hero.png" alt="Borzoi Track Activity" />
</div>

<Note>
  **License:** Borzoi uses Apache-2.0 for code and CC-BY-4.0 for model weights and may require explicit attribution when utilized. Please refer to the [code license](https://github.com/calico/borzoi/blob/main/LICENSE) and [model weights license](https://huggingface.co/johahi/borzoi-replicate-0) for full terms.
</Note>

<p class="entity-disclaimer">This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.</p>

<hr class="entity-rule" />

<input type="radio" name="tab-constraint-borzoi-track-activity" id="none-constraint-borzoi-track-activity" class="tab-radio-input" />

<input type="radio" name="tab-constraint-borzoi-track-activity" id="tools-constraint-borzoi-track-activity" class="tab-radio-input" defaultChecked />

<input type="radio" name="tab-constraint-borzoi-track-activity" id="source-constraint-borzoi-track-activity" class="tab-radio-input" />

<input type="radio" name="tab-constraint-borzoi-track-activity" id="cite-constraint-borzoi-track-activity" class="tab-radio-input" />

<div class="tool-tab-bar"><span class="tool-tab-wrap"><label for="tools-constraint-borzoi-track-activity" class="tool-tab tab-open badge-tools"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><rect width="7" height="7" x="3" y="3" rx="1" /><rect width="7" height="7" x="14" y="3" rx="1" /><rect width="7" height="7" x="14" y="14" rx="1" /><rect width="7" height="7" x="3" y="14" rx="1" /></svg> Tools Used</label><label for="none-constraint-borzoi-track-activity" class="tool-tab tab-close badge-tools"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><rect width="7" height="7" x="3" y="3" rx="1" /><rect width="7" height="7" x="14" y="3" rx="1" /><rect width="7" height="7" x="14" y="14" rx="1" /><rect width="7" height="7" x="3" y="14" rx="1" /></svg> Tools Used</label></span> <span class="tool-tab-wrap"><label for="source-constraint-borzoi-track-activity" class="tool-tab tab-open badge-source"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="16 18 22 12 16 6" /><polyline points="8 6 2 12 8 18" /></svg> Source</label><label for="none-constraint-borzoi-track-activity" class="tool-tab tab-close badge-source"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="16 18 22 12 16 6" /><polyline points="8 6 2 12 8 18" /></svg> Source</label></span> <span class="tool-tab-wrap"><label for="cite-constraint-borzoi-track-activity" class="tool-tab tab-open badge-cite"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M3 21c3 0 7-1 7-8V5c0-1.25-.756-2.017-2-2H4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2 1 0 1 0 1 1v1c0 1-1 2-2 2s-1 .008-1 1.031V20c0 1 0 1 1 1z" /><path d="M15 21c3 0 7-1 7-8V5c0-1.25-.757-2.017-2-2h-4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2h.75c0 2.25.25 4-2.75 4v3c0 1 0 1 1 1z" /></svg> Cite</label><label for="none-constraint-borzoi-track-activity" class="tool-tab tab-close badge-cite"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M3 21c3 0 7-1 7-8V5c0-1.25-.756-2.017-2-2H4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2 1 0 1 0 1 1v1c0 1-1 2-2 2s-1 .008-1 1.031V20c0 1 0 1 1 1z" /><path d="M15 21c3 0 7-1 7-8V5c0-1.25-.757-2.017-2-2h-4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2h.75c0 2.25.25 4-2.75 4v3c0 1 0 1 1 1z" /></svg> Cite</label></span></div>

<a href="/docs/tools/sequence-scoring/borzoi" class="tab-panel tools-panel tools-panel-single" data-tab="tools-constraint-borzoi-track-activity">
  <div class="tools-single-card">
    <img noZoom src="https://proto-bio.github.io/proto-assets/images/tool/borzoi/social.png" alt="" loading="lazy" />
  </div>

  <span class="panel-goto-btn tools-goto-btn"><span><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M5 12h14" /><path d="m12 5 7 7-7 7" /></svg> Go to Tool Page</span></span>
</a>

<a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/sequence_annotation/borzoi_track_activity_constraint.py#L185" target="_blank" class="tab-panel source-panel" data-tab="source-constraint-borzoi-track-activity">
  <div class="source-info">
    <img noZoom src="https://github.com/evo-design.png?size=40" class="source-avatar" width="36" height="36" />

    <span class="source-path">evo-design/proto-language<span class="source-subpath">/proto\_language/constraint/sequence\_annotation/borzoi\_track\_activity\_constraint.py</span></span>
  </div>

  <span class="panel-goto-btn source-goto-btn"><span><svg width="14" height="14" viewBox="0 0 24 24" fill="currentColor"><path d="M12 0C5.37 0 0 5.37 0 12c0 5.31 3.435 9.795 8.205 11.385.6.105.825-.255.825-.57 0-.285-.015-1.23-.015-2.235-3.015.555-3.795-.735-4.035-1.41-.135-.345-.72-1.41-1.23-1.695-.42-.225-1.02-.78-.015-.795.945-.015 1.62.87 1.845 1.23 1.08 1.815 2.805 1.305 3.495.99.105-.78.42-1.305.765-1.605-2.67-.3-5.46-1.335-5.46-5.925 0-1.305.465-2.385 1.23-3.225-.12-.3-.54-1.53.12-3.18 0 0 1.005-.315 3.3 1.23.96-.27 1.98-.405 3-.405s2.04.135 3 .405c2.295-1.56 3.3-1.23 3.3-1.23.66 1.65.24 2.88.12 3.18.765.84 1.23 1.905 1.23 3.225 0 4.605-2.805 5.625-5.475 5.925.435.375.81 1.095.81 2.22 0 1.605-.015 2.895-.015 3.3 0 .315.225.69.825.57A12.02 12.02 0 0024 12c0-6.63-5.37-12-12-12z" /></svg> View source</span></span>
</a>

<div class="tab-panel cite-panel" data-tab="cite-constraint-borzoi-track-activity">
  <div class="cite-code-wrap">
    ```bibtex theme={null}
    @article{linder2025borzoi,
      title={Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation},
      author={Linder, Johannes and Srivastava, Divyanshi and Yuan, Han and Agarwal, Vikram and Kelley, David R},
      journal={Nature Genetics},
      volume={57},
      number={4},
      pages={949--961},
      year={2025},
      publisher={Nature Publishing Group},
      doi={10.1038/s41588-024-02053-6}
    }
    ```
  </div>

  <span class="panel-goto-btn cite-copy-btn"><span><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M3 21c3 0 7-1 7-8V5c0-1.25-.756-2.017-2-2H4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2 1 0 1 0 1 1v1c0 1-1 2-2 2s-1 .008-1 1.031V20c0 1 0 1 1 1z" /><path d="M15 21c3 0 7-1 7-8V5c0-1.25-.757-2.017-2-2h-4c-1.25 0-2 .75-2 1.972V11c0 1.25.75 2 2 2h.75c0 2.25.25 4-2.75 4v3c0 1 0 1 1 1z" /></svg> Copy citation</span></span>
</div>

<div class="entity-contributors"><span class="entity-contributors-label">Constraint contributors</span><span class="entity-contributors-people"><a class="entity-contributor" href="https://github.com/brianhie" target="_blank" rel="noopener" title="brianhie: 1 commit"><img noZoom class="entity-contributor-avatar" src="https://avatars.githubusercontent.com/u/6365340?v=4&s=64" alt="" loading="lazy" /><span class="entity-contributor-login">brianhie</span></a></span></div>
Score target proposals for selected Borzoi output tracks.

## API Reference

<div class="api-model-section api-model-static api-config-section">
  <div class="api-model-header"><span class="api-model-badge api-config-badge">Config</span><span class="api-model-name">BorzoiTrackActivityConfig</span><a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/sequence_annotation/borzoi_track_activity_constraint.py#L54" target="_blank" class="func-table-btn func-source-btn api-model-source"><svg width="12" height="12" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="16 18 22 12 16 6" /><polyline points="8 6 2 12 8 18" /></svg> Source</a></div>

  Configuration for Borzoi track-activity scoring.

  <ParamField path="organism" type="enum" default="human">
    Borzoi species head to use: human or mouse.

    Options: `human`, `mouse`
  </ParamField>

  <ParamField path="borzoi_output_tracks" type="List[integer]" default="[0]">
    Borzoi output track IDs to average before scoring.
  </ParamField>

  <ParamField path="score_intervals" type="array">
    Optional target-relative intervals to score. If omitted, scores the full target segment.
  </ParamField>

  <ParamField path="direction" type="enum" default="maximize">
    Whether high activity or low activity is preferred.

    Options: `maximize`, `minimize`
  </ParamField>

  <ParamField path="activity_threshold" type="number" default="200.0">
    Activity value treated as saturating success for the objective.
  </ParamField>

  <ParamField path="borzoi_ensemble_reduce_method" type="enum" default="mean">
    How to combine Borzoi replicate signals.

    Options: `mean`, `min`, `std`, `lcb`
  </ParamField>

  <ParamField path="device" type="string" default="cuda">
    CUDA device for Borzoi inference.
  </ParamField>

  <ParamField path="batch_size" type="integer" default="1">
    Candidate sequences per Borzoi model batch.
  </ParamField>

  <ParamField path="trim_prefix_bp" type="integer" default="0">
    Leading target bases to ignore before Borzoi scoring.
  </ParamField>
</div>

## Usage

```python python icon="python" theme={null}
from proto_language.core import Constraint
from proto_language.constraint import borzoi_track_activity_constraint, BorzoiTrackActivityConfig

constraint = Constraint(
    inputs=[segment],
    function=borzoi_track_activity_constraint,
    function_config=BorzoiTrackActivityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()
```

## Metadata

| Property        | Value                              |
| --------------- | ---------------------------------- |
| Key             | `borzoi-track-activity`            |
| Function        | `borzoi_track_activity_constraint` |
| Category        | `sequence_annotation`              |
| Mode            | `discrete`                         |
| Uses GPU        | `True`                             |
| Supported Types | `dna`                              |
