Description of the genome query for

ORFs more closely related than expected

The user is prompted to enter a pair of genomes, which are assumed to be sister taxa, or if not, the tree is pruned in order to make them sister taxa. For clarity below, we can refer to these as genomes A and B.

Then, all sequences from outgroup genome C that match more closely to A or to B than A matches with B, are returned. The user provides a threshold proportional distance from a pull-down menu, that specifies just how much closer the match must be.

Example:

If one selects Escherichia coli CFT073 and Yersinia pestis CO92 as the "sisters", all genomes bracketed by this pair are pruned from the tree, leaving only outgroups. Next, suppose that one selects 0.20 as the proportional distance threshold. The query returns all ORFs from E. coli CFT073 and from Y. pestis CO92 where the outgroup genome's ORF is more closely related by a factor of 5 (i.e., 1.0 / 0.2) either to the E. coli or to the Y. pestis ORF, than E. coli's ORF is related to Y. pestis's. When the proportional distance threshold is high (e.g., 0.8), paralogies will turn up in addition to candidate lateral gene transfer events, but when the threshold is low and stringent (e.g. 0.2), only LGT events should come through. We suggest that the user then construct full, multiple alignment-based trees with sequences retrieved using the Retrieve Sequences query.