SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models

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書誌事項

公開日
2024-07-25
資源種別
journal article
権利情報
  • https://creativecommons.org/licenses/by/4.0
  • https://creativecommons.org/licenses/by/4.0
DOI
  • 10.1186/s13059-024-03298-4
公開者
Springer Science and Business Media LLC

説明

<jats:title>Abstract</jats:title> <jats:p> Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by time-consuming all-versus-all alignments and the existence of proteins with complex domain architectures. Here, we present a substantial update of SonicParanoid, where a gradient boosting predictor halves the execution time and a language model doubles the recall. Application to empirical large-scale and standardized benchmark datasets shows that SonicParanoid2 is much faster than comparable methods and also the most accurate. SonicParanoid2 is available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://gitlab.com/salvo981/sonicparanoid2">https://gitlab.com/salvo981/sonicparanoid2</jats:ext-link> and <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://zenodo.org/doi/10.5281/zenodo.11371108">https://zenodo.org/doi/10.5281/zenodo.11371108</jats:ext-link> . </jats:p>

収録刊行物

  • Genome Biology

    Genome Biology 25 (1), 2024-07-25

    Springer Science and Business Media LLC

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