The paper introduces Blast2GO, a comprehensive bioinformatics tool for functional annotation and data mining in plant genomics research. Blast2GO is designed to facilitate the functional annotation of novel sequence data, particularly in nonmodel species, by optimizing function transfer from homologous sequences through an elaborate algorithm that considers similarity, homology extension, database choice, GO hierarchy, and original annotation quality. The tool includes features for visualization, management, and statistical analysis of annotation results, such as gene set enrichment analysis. It supports various controlled vocabularies, including GO, InterPro, enzyme codes, KEGG pathways, and GOSlim. Blast2GO is user-friendly, easy to install, and has been widely adopted by research labs, with over 100 users worldwide and references in over thirty peer-reviewed publications. The paper also provides a detailed description of the annotation procedure, including blast, mapping, and annotation steps, and highlights the tool's flexibility and data mining capabilities. A use case on the functional annotation of the Soybean Affymetrix GeneChip is presented to illustrate the application's features and performance.The paper introduces Blast2GO, a comprehensive bioinformatics tool for functional annotation and data mining in plant genomics research. Blast2GO is designed to facilitate the functional annotation of novel sequence data, particularly in nonmodel species, by optimizing function transfer from homologous sequences through an elaborate algorithm that considers similarity, homology extension, database choice, GO hierarchy, and original annotation quality. The tool includes features for visualization, management, and statistical analysis of annotation results, such as gene set enrichment analysis. It supports various controlled vocabularies, including GO, InterPro, enzyme codes, KEGG pathways, and GOSlim. Blast2GO is user-friendly, easy to install, and has been widely adopted by research labs, with over 100 users worldwide and references in over thirty peer-reviewed publications. The paper also provides a detailed description of the annotation procedure, including blast, mapping, and annotation steps, and highlights the tool's flexibility and data mining capabilities. A use case on the functional annotation of the Soybean Affymetrix GeneChip is presented to illustrate the application's features and performance.