Frequenty Asked Questions - Comparative Genomics

What do Target % ID and Query % ID mean in the Comparative Genomics views of the Ensembl Genome browsers?

Query % ID and Target % ID are reported on Comparative Genomics views of the Ensembl Genomes browser such as the 'Orthologues' page (see an example here). If you are searching for one gene in arabidopsis and looking for its homologue in another species such as maize, the query % ID refers to the percentage of the sequence in the query species (Arabidopsis) that matches to the homologue (the maize protein). Target % ID refers to the percentage of the sequence in the target species (maize) that matches to the query sequence (Arabidopsis).
It can be helpful to think of a query sequence (Arabidopsis protein) of length 100 amino acids, and a target sequence (maize protein) of length 50 amino acids. Assume that the sequence of 50 amino acids are identical between the two proteins. In this case, Query % ID will be 50%, and Target % ID will be 100%.

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