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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.

2025-04-01 bioinformatics
10.1101/2025.03.30.646211 bioRxiv
Show 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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