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bioRxiv · 10.1101/2023.05.14.540736

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

Cosentino, S.·Iwasaki, W.
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Abstract

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 showed that SonicParanoid2 is up to 18X faster than comparable methods and also the most accurate. SonicParanoid2 is available at https://gitlab.com/salvo981/sonicparanoid2

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Cosentino, S., Iwasaki, W.. 2023-05-15. SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models. https://doi.org/10.1101/2023.05.14.540736

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