Blast2GO is a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the Gene Ontology (GO) vocabulary. It optimizes function transfer from homologous sequences using an algorithm that considers similarity, homology extension, database choice, GO hierarchy, and original annotation quality. The tool includes functions for visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. It supports InterPro, enzyme codes, KEGG pathways, GO DAGs, and GOSlim. Blast2GO is suitable for plant genomics research due to its versatility, ease of installation, and user-friendly interface. The tool is designed for biology researchers working on functional genomics projects in labs with limited bioinformatics support. It is a multiplatform Java application accessible via Java Webstart, ensuring automatic updates and efficient user access. Blast2GO is used for high-throughput annotation of novel sequences, with the ability to process large datasets and provide interactive results. It supports various databases and annotation strategies, including homology transfer, and allows for flexible annotation using different vocabularies such as GO, EC, InterPro, and KEGG. The annotation process involves three steps: blast to find homologous sequences, mapping to collect GO terms, and annotation to assign functional terms. The tool includes functions for modulation of annotations, such as using additional vocabularies, GOSlim mapping, and manual curation. Visualization and data mining functions allow for the evaluation of annotation results, including statistical charts, sequence coloring, and combined graphs. Blast2GO also includes enrichment analysis to identify statistically significant functional classes between two sets of sequences. It supports the integration of InterProScan and Annex for annotation augmentation, and provides tools for manual curation of annotations. The tool is used in various plant genomics projects, including the annotation of the Soybean Affymetrix GeneChip, demonstrating its effectiveness in functional genomics research. Blast2GO is a valuable resource for plant genomics due to its comprehensive features, ease of use, and ability to handle large datasets.Blast2GO is a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the Gene Ontology (GO) vocabulary. It optimizes function transfer from homologous sequences using an algorithm that considers similarity, homology extension, database choice, GO hierarchy, and original annotation quality. The tool includes functions for visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. It supports InterPro, enzyme codes, KEGG pathways, GO DAGs, and GOSlim. Blast2GO is suitable for plant genomics research due to its versatility, ease of installation, and user-friendly interface. The tool is designed for biology researchers working on functional genomics projects in labs with limited bioinformatics support. It is a multiplatform Java application accessible via Java Webstart, ensuring automatic updates and efficient user access. Blast2GO is used for high-throughput annotation of novel sequences, with the ability to process large datasets and provide interactive results. It supports various databases and annotation strategies, including homology transfer, and allows for flexible annotation using different vocabularies such as GO, EC, InterPro, and KEGG. The annotation process involves three steps: blast to find homologous sequences, mapping to collect GO terms, and annotation to assign functional terms. The tool includes functions for modulation of annotations, such as using additional vocabularies, GOSlim mapping, and manual curation. Visualization and data mining functions allow for the evaluation of annotation results, including statistical charts, sequence coloring, and combined graphs. Blast2GO also includes enrichment analysis to identify statistically significant functional classes between two sets of sequences. It supports the integration of InterProScan and Annex for annotation augmentation, and provides tools for manual curation of annotations. The tool is used in various plant genomics projects, including the annotation of the Soybean Affymetrix GeneChip, demonstrating its effectiveness in functional genomics research. Blast2GO is a valuable resource for plant genomics due to its comprehensive features, ease of use, and ability to handle large datasets.