> ## 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.

# Gene Annotation

> Search and annotate sequences against databases

Search and annotate sequences to discover what they are. These tools find homologs in
reference databases, label protein domains and families, and identify functional elements
such as CRISPR arrays, microRNA target sites, and promoters, turning an unannotated sequence
into a set of functional and evolutionary hypotheses.

* **Input:** a nucleotide or protein sequence.
* **Output:** annotated features and database hits, such as homologs, protein domains, and functional elements, with significance scores.

<div class="tool-catalog-grid">
  <a href="/docs/tools/gene-annotation/crispr-tracr-rna" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/crispr_tracr_rna/carousel.png" alt="" loading="lazy" />
  </a>

  <a href="/docs/tools/gene-annotation/meme" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/meme/carousel.png" alt="" loading="lazy" />

    <div class="tool-card-org-row"><span class="tool-card-org" style={{background: "#003366"}} title="University of Nevada, Reno"><img src="https://mintcdn.com/bio-pro/rW-ZVHoYhZw2v7T_/assets/images/cached/5629497fc5f9.png?fit=max&auto=format&n=rW-ZVHoYhZw2v7T_&q=85&s=0152a7b2026578de05c05152d8d36b92" alt="" class="tool-card-org-logo" width="330" height="108" data-path="assets/images/cached/5629497fc5f9.png" /> UNR</span> <span class="tool-card-org" style={{background: "#4B2E83"}} title="University of Washington">UW</span> <span class="tool-card-org" style={{background: "#51247A"}} title="University of Queensland"><img src="https://mintcdn.com/bio-pro/rW-ZVHoYhZw2v7T_/assets/images/cached/a4e83fbbeb06.png?fit=max&auto=format&n=rW-ZVHoYhZw2v7T_&q=85&s=3378fc54f11fc74455207f45eee61ff4" alt="" class="tool-card-org-logo" width="180" height="180" data-path="assets/images/cached/a4e83fbbeb06.png" /> UQ</span> <span class="tool-card-org" style={{background: "#182B49"}} title="University of California, San Diego"><img src="https://mintcdn.com/bio-pro/rW-ZVHoYhZw2v7T_/assets/images/cached/ec1fd211cd18.png?fit=max&auto=format&n=rW-ZVHoYhZw2v7T_&q=85&s=a9bd8bd71144d343f19d8d950a5561d9" alt="" class="tool-card-org-logo" width="330" height="332" data-path="assets/images/cached/ec1fd211cd18.png" /> UCSD</span></div>
  </a>

  <a href="/docs/tools/gene-annotation/minced" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/minced/carousel.png" alt="" loading="lazy" />
  </a>

  <a href="/docs/tools/gene-annotation/miranda" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/miranda/carousel.png" alt="" loading="lazy" />

    <div class="tool-card-org-row"><span class="tool-card-org" style={{background: "#1A5CA8"}} title="Memorial Sloan Kettering Cancer Center"><img src="https://mintcdn.com/bio-pro/UeudeF7pW-Dj-pIN/assets/images/cached/069c915f9010.png?fit=max&auto=format&n=UeudeF7pW-Dj-pIN&q=85&s=0ec54d6d54fe316ca4a008d7c769d7c9" alt="" class="tool-card-org-logo" width="200" height="200" data-path="assets/images/cached/069c915f9010.png" /> MSKCC</span></div>
  </a>

  <a href="/docs/tools/gene-annotation/promoter-calculator" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/promoter_calculator/carousel.png" alt="" loading="lazy" />
  </a>

  <a href="/docs/tools/gene-annotation/pyhmmer" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/pyhmmer/carousel.png" alt="" loading="lazy" />
  </a>
</div>