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Description of the genome query for

Find Ubiquitous Genes

For each ORF in the chosen genome, or for each ORF in the "Results from my last query,"
a search is made in each target genome for ORFs that match, or reciprocally best match, the ORF in question. The genomes considered are those that belong to the group previously defined by the user. ORFs from the selected genome are returned if they match a sufficient number of genomes (as specified by the user) in this group.
Alternatively, the user may select an option to search for ubiquitous genes from the perspective of each member of the defined group. In that case, the pull-down menu of genomes is ignored.
In determining if a match is a reciprocal best match, near-ties are considered if the non-best match is close to the best match in score, using a tolerance supplied by the user.

This query might be useful for identifying the genes that are core to a clade. Comparing lists of such genes, from different clades or from hierarchies of clades, should be especially interesting. Note however, that the search is biased towards evolutionarily conserved (slowly evolving) genes, that it is sensitive to neglected annotation, and that it is sensitive to matches that straddle the BLASTP cutoff.

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