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bioRxiv · 10.1101/2025.03.30.646211

GeneWhisperer: Enhancing manual genome annotation with large language models

Li, X.·Whan, A. P.·McNeil, M.·Andrew, S. C.·Dai, X.·Fechner, M.·Paris, C.·Suchecki, R.
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Abstract

Genome annotation is critical for understanding functional elements within genomes. Manual curation is a common practice for identifying the functions of genes, particularly those missed by automated annotation pipelines. However, this process is notoriously labour-intensive and time-consuming. In response to these challenges, we present GeneWhisperer, an innovative assistant system designed to facilitate the manual gene functional annotation process. Utilizing a large language model (LLM) agent, GeneWhisperer provides users access to tools appropriate for specific curation tasks in genome annotation. Featuring a conversational interface, GeneWhisperer fosters effective collaboration between human experts and AI. By synergizing the capabilities of AI with human expertise, GeneWhisperer offers a promising approach to advancing our understanding of gene functions and streamlining the gene annotation process.

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Li, X., Whan, A. P., McNeil, M., Andrew, S. C., Dai, X., Fechner, M., Paris, C., Suchecki, R.. 2025-04-01. GeneWhisperer: Enhancing manual genome annotation with large language models. https://doi.org/10.1101/2025.03.30.646211

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