Gaia: An AI-enabled genomic context-aware platform for protein sequence annotation.

ABSTRACT: Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based

SUBMITTER: Jha N 

PROVIDER: S-EPMC12180486 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature