> ## 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.

# TargetScan Seed Site

> Score miRNA target-site burden by TargetScan canonical seed-match site typing (6mer/7mer/8mer).

<div class="page-hero">
  <img class="page-hero-banner" src="https://proto-bio.github.io/proto-assets/images/constraint/targetscan-site/hero.png" alt="TargetScan Seed Site" />
</div>

<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" />

<div class="tool-tab-bar entity-source-bar"><span class="tool-tab-wrap"><span class="tool-tab badge-source entity-source-tab"><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</span></span></div>

<a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/sequence_annotation/targetscan_site_constraint.py#L210" target="_blank" class="tab-panel source-panel entity-source-panel">
  <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/targetscan\_site\_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="entity-contributors"><span class="entity-contributors-label">Constraint contributors</span><span class="entity-contributors-people"><a class="entity-contributor" href="https://github.com/adititm" target="_blank" rel="noopener" title="adititm: 1 commit"><img noZoom class="entity-contributor-avatar" src="https://avatars.githubusercontent.com/u/61667248?v=4&s=64" alt="" loading="lazy" /><span class="entity-contributor-login">adititm</span></a></span></div>
Score miRNA seed-match site burden using TargetScan's canonical site definitions.

For each target sequence and each miRNA, canonical seed-match sites are detected and
summed with per-site-type and per-miRNA weights into an aggregate burden, bounded by
`repression_threshold`. `direction='maximize'` rewards installing sites (low score
when burden is high); `direction='minimize'` rewards escaping them.

## 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">TargetScanSiteConfig</span><a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/constraint/sequence_annotation/targetscan_site_constraint.py#L53" 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 TargetScan canonical seed-match site scoring.

  <ParamField path="mirna_queries" type="List[string]" required>
    miRNA query sequences (>= 8 nt) whose seed (positions 2-8) defines target sites.
  </ParamField>

  <ParamField path="mirna_ids" type="array">
    Optional identifiers for miRNA queries.
  </ParamField>

  <ParamField path="mirna_weights" type="array">
    Optional nonnegative per-miRNA expression weights matching the miRNA query order.
  </ParamField>

  <ParamField path="direction" type="enum" default="maximize">
    Whether predicted miRNA site burden should be high or low.

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

  <ParamField path="repression_threshold" type="number" default="2.0">
    Aggregated site-burden score treated as saturating success.
  </ParamField>

  <ParamField path="site_type_weights" type="object">
    Per-site-type strengths for 8mer/7mer-m8/7mer-A1/6mer.
  </ParamField>

  <ParamField path="include_6mer" type="boolean" default="True">
    Whether to count weak 6mer sites (set False to require >= 7mer).
  </ParamField>
</div>

<div class="api-model-section api-model-static api-output-section">
  <div class="api-model-header"><span class="api-model-badge api-output-badge">Returns</span><span class="api-model-name">ConstraintOutput</span></div>

  One result per sequence. `score` is in `[0, 1]`
  (0.0 = objective fully satisfied). `metadata` carries the aggregated
  `targetscan_repression_score`, `targetscan_num_sites`, and a per-site
  list with miRNA id, site type, weighted strength, and 1-indexed coordinates.
</div>

## Usage

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

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

scores = constraint.evaluate()
```

## Metadata

| Property        | Value                        |
| --------------- | ---------------------------- |
| Key             | `targetscan-site`            |
| Function        | `targetscan_site_constraint` |
| Category        | `sequence_annotation`        |
| Mode            | `discrete`                   |
| Uses GPU        | `False`                      |
| Supported Types | `dna`, `rna`                 |