The article introduces the Blast2GO suite, an integrated and biologist-oriented solution for high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology (GO) vocabulary. The suite combines various annotation strategies and tools, provides numerous graphical features, and includes general sequence management capabilities. Key features include hit coverage filters, GO-slim, Annex, enzyme code annotations, KEGG pathway visualization, InterProScan, and manual curation tools. The article also discusses the impact of different annotation styles on annotation performance, manual curation, cis annotation, and functional genomics research. The evaluation tasks include annotation performance, manual curation, cis annotation, and functional genomics, with results showing that the choice of annotation style influences the results in enrichment analyses but a common biological message is obtained across different configurations. The Blast2GO suite is designed to be user-friendly, flexible, and accessible, making it suitable for middle-sized labs conducting functional genomics research.The article introduces the Blast2GO suite, an integrated and biologist-oriented solution for high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology (GO) vocabulary. The suite combines various annotation strategies and tools, provides numerous graphical features, and includes general sequence management capabilities. Key features include hit coverage filters, GO-slim, Annex, enzyme code annotations, KEGG pathway visualization, InterProScan, and manual curation tools. The article also discusses the impact of different annotation styles on annotation performance, manual curation, cis annotation, and functional genomics research. The evaluation tasks include annotation performance, manual curation, cis annotation, and functional genomics, with results showing that the choice of annotation style influences the results in enrichment analyses but a common biological message is obtained across different configurations. The Blast2GO suite is designed to be user-friendly, flexible, and accessible, making it suitable for middle-sized labs conducting functional genomics research.