In the course of FlyBase analysis, Gene Ontology (GO) terms are assigned to genes on the basis of sequence similarity to homologous sequences using the evidence code 'inferred from sequence or structural similarity' (ISS).
Following the rules established by the GO reference genome project, it is mandatory to include a database cross-reference in the GO annotation that identifies the similar gene/gene product. To avoid circular inferences, the similar gene must be experimentally characterised; the GO term should only be assigned if the similar gene can be annotated with the same term (or a more specific child term) using an experimental evidence code (inferred from direct assay, IDA; inferred from mutant phenotype, IMP; inferred from genetic interaction, IGI, inferred from physical interaction, IPI; inferred from expression pattern, IEP).
Homologous sequences are identified by BLAST and the significance of matches judged on a case-by-case basis by the FlyBase GO curator. This reference corresponds to annotations made to GO_REF:0000024.