Overview of terms used in this server.
Transcript
A predicted transcript. Transcripts are identified by integers, that, due to filtering, need not be consecutive. They might also be external identifiers, if we have used gene sets from ENSEMBL or FLYBASE
Gene
A collection of transcripts. Transcripts sharing one identical exon constitute a gene. Genes are identified by integers, that, due to filtering, need not be consecutive. They might also be external identifiers, if we have used gene sets from ENSEMBL or FLYBASE.
Orthologous group
A set of genes that are in orthologous or in-paralogous relationships to each other. These groups are are result of splitting clusters according to the species phylogeny. Orthologous groups are identified by consecutive numerical identifiers from 1 to 9999.
Simple ortholog set
An orthologous set contains exactly one gene of each species. Simple orthologous sets are identified by consecutive numerical identifiers from 1 to 99495.
Cluster
Cluster of pairwise orthologous sequences. Clusters are split using outgroups/outparalogs into orthologous groups. Cluster are identified by consecutive numerical identifier from 1 to 12900.
Phylogenetic pattern
Phylogenetic patterns are a short-hand notation for denoting absences and presences of species in orthologous groups and simple orthologous sets. The length of the pattern should correspond to the number species in the clade. The symbols and their meaning are:
ClassSymbolMeaning
Orthologous groups +Species is present, i.e., there is at least one gene of this species in this ortholog group.
0No genes of this species are present in this ortholog group.
Simple orthologous sets 1Species is present and contains exactly one gene.
-Species is ignored.