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bioRxiv · 10.64898/2025.12.02.690645

gffutilsAI: An AI-Agent for Interactive Genomic Feature Exploration in GFF files

Bassi, S.·Gonzalez, C.·Yang, T.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWThe General Feature Format (GFF) is widely used to represent genomic annotations, but its hierarchical, multi-attribute structure makes manual querying and analysis challenging. Existing libraries such as gffutils provide programmatic interfaces, yet they require coding proficiency. gffutilsAI is a novel AI-powered command-line agent that enables researchers to perform interactive, natural-language-driven exploration of GFF files. Built on top of the gffutils library and the Strands AI agent framework, gffutilsAI integrates local and cloud-based large language models (LLMs) such as Llama 3.1, GPT-5, and Claude 3.5 to translate human queries into executable actions. The tool supports coordinate-based queries, attribute and GO searches, hierarchical traversal, statistical summaries, and CSV export, offering a new paradigm for accessible conversational genomics.

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Bassi, S., Gonzalez, C., Yang, T.. 2025-12-05. gffutilsAI: An AI-Agent for Interactive Genomic Feature Exploration in GFF files. https://doi.org/10.64898/2025.12.02.690645

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