D286 Nucleic Acids Research, 2011, Vol. 39, Database issue Figure 2. Screenshot of a sample result page, featuring functional Gene Ontology (GO), InterPro and phenotype annotations, as well as evolutionary related groups, phyletic proﬁle and relative divergence among orthologs. performed at speciﬁc radiation points by selecting a node of the interactive species trees. Selecting a node en- compassing only a few closely related species will focus the search results on more ﬁne-grained orthologous groups of mostly one-to-one relations. Moving toward the root of the tree will include more distantly related species and will generally retrieve more inclusive orthologous groups that contain all the descendants of the ancestral gene. Text searches. OrthoDB enables relevant data retrieval through speciﬁc queries using protein, gene, InterPro or GO identiﬁers, or more general searches with keywords, names or synonyms, descriptor terms or phrases. Gene annotations sourced from UniProt, supplemented with data from speciﬁc resources for representative model organisms from each lineage, provide rich annotations that facilitate comprehensive database searching. The text search feature provides additional ﬂexibility using simple logical operator syntax to build complex queries; e.g. to optionally include variations of a term, or to exclude terms (Supplementary Table S3). In addition, speciﬁc protein domain architectures may be queried with a comma-separated N- to C-terminus ordered list of InterPro identiﬁers. Copy-number proﬁles. OrthoDB features the ability to search for orthologous groups with speciﬁc phyletic proﬁles to retrieve groups matching speciﬁc copy-number criteria such as all single-copy or all multi-copy orthologs. Combining the criteria of absent, present, single-copy, multi-copy or no restriction, for each species within a selected clade can generate numerous variations of user-deﬁned phyletic proﬁles for database querying. These proﬁle query options are extended through a selec- tion of predeﬁned common proﬁles with more relaxed search criteria, e.g. single-copy orthologs but allowing for a gene loss or duplication event in one species. Sequence similarity. The BLAST search facility ensures that data interrogation is not limited by the coverage of detailed gene annotations. The relevant data of the orthologous group closest to the root-level are returned if a protein sequence match with a signiﬁcant BLAST hit