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<p>Protein functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to ~1000 animal proteomes, FANTASIA predicts functions to virtually all proteins, including up to 50% that remained unannotated by traditional homology-based methods. This enables the discovery of novel gene functions, enhancing our understanding of molecular evolution and organismal biology. FANTASIA holds particular promise for functional discovery in non-model taxa, offering advantages over homology-based tools in sensitivity and generalizability. FANTASIA is available on GitHub at <a href="https://github.com/CBBIO/FANTASIA">https://github.com/CBBIO/FANTASIA</a>.</p><p></p>

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FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年8月14日

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  • Gemma I. Martínez-Redondo,
  • Francisco M. Perez-Canales,
  • Belén Carbonetto,
  • José M. Fernández,
  • Israel Barrios-Núñez,
  • Marçal Vázquez-Valls,
  • Ildefonso Cases,
  • Ana M. Rojas,
  • Rosa Fernández

摘要

Protein functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to ~1000 animal proteomes, FANTASIA predicts functions to virtually all proteins, including up to 50% that remained unannotated by traditional homology-based methods. This enables the discovery of novel gene functions, enhancing our understanding of molecular evolution and organismal biology. FANTASIA holds particular promise for functional discovery in non-model taxa, offering advantages over homology-based tools in sensitivity and generalizability. FANTASIA is available on GitHub at https://github.com/CBBIO/FANTASIA.