Frequently Asked Questions

Q.  How can I get a list of genes that do not have orthologs in one or more species?
A.  If you want to obtain genes that do not have orthologs in one other species, you can use the Obtain Orthologs Between Two Genomes search. Under Optional - only return unique genes for: select the species to obtain genes for. Note: inparalogs are included as unique genes, but are indicated as inparalogs in the results. If you want to obtain genes that do not have orthologs in multiple species, use the Compare Genome to Orthologs in Comparison Genomes search. From the results page, click on the Gene Filter Settings tab. In the filter form, select Ortholog is absent for all species that you want to use to exclude genes in your index genome when an ortholog exists. This will give you genes that do not have orthologs in ALL of the genomes that are selected.
Q.  Why doesn't this ortholog/analysis have Ortholuge classifications?
A.  Ortholuge uses an outgroup species to compute the phylogenetic ratios that it uses to observe the ortholog divergence. If there is no suitable outgroup species, only reciprocal-best-BLAST predictions will be available for the analysis.

When there is an available outgroup species, a pair of orthologous genes will have an Ortholuge classification when there is an gene in the outgroup genome that is orthologous to the two orthologs in the comparison species. If this outgroup gene is missing, no Ortholuge evaluation will be available.
Q.  Can I view the gene context (or neighbouring genes) for an ortholog?
A.  We provide gene context views in the Obtain Orthologs For a Single Gene and Obtain Orthologs Between Two Genomes searches. Check off Yes under Show gene context to display the gene context in the result table.
Q.  What do the gene colors signify in the gene context images?
A.  Genes are colored according to their subcellular localization. Red, cytoplasmic; yellow, periplasmic membrane; orange, cytoplasmic membrane; green, outer membrane; blue, extracellular; grey, unknown.
Q.  What's the difference between an ortholog group and obtaining orthologs for a gene?
A.  Ortholog groups are obtained through the Obtain Pre-computed Orthologs Groups for a Gene search, orthologs for a single gene are obtained through the Obtain Orthologs For a Single Gene

Ortholog groups are transitive. That is, they contain all ortholog connections linked to any of the genes in the group (i.e. the orthologs of the ortholog, and so on). Orthologs for a single gene only contain genes directly linked to the gene of interest through an orthologous relationship. Ortholog groups are broader in scope and are better suited for examining the distribution of a gene, while obtaining orthologs for single gene can be limited to specific species and is ideal for more focused queries.

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