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Description of the genome query for

List Named Ubiquitous Genes

This analysis makes use of the concept of "consensus gene name", in finding genes that are ubiquitously distributed among sequenced genomes. An ORF's consensus gene name is defined as being the most common annotated name from among the set consisting of itself and all of its reciprocal best matches (using a BLASTP cutoff expectation value of 1.0e-3) in other genomes. Once each ORF from each genome has been assigned its consensus name, a tally is made of what names occur in what genomes. It is furthermore assumed that a name present in at least two-thirds of genomes represents an orthologous set, whereas it cannot safely be assumed that a name present in a minority of genomes does not include homonyms. (Given our desire to find ubiquitous genes, this latter point is moot.) It is then quite straightforward to display ubiquitous genes (consensus gene names) from a selected subset of all genomes.

This query is similar to Find Ubiquitous Genes, except that this query is genome-independent and relies on consensus gene names, whereas "Find Ubiquitous Genes" is genome-dependent and therefore looks for ubiquitous genes from each genome's own perspective. The former is more useful for finding so-called "core genes", whereas the latter is necessary if one wants to chain queries together.