Description of the genome query for

Gene order conservation

From the list of ORFs from the first chosen genome, sorted by locus position, the query identifies which pairs of neighboring ORFs (1-4 ORFs' distance from one another) match a pair of neighboring ORFs (1-4 ORFs' distance from one another) in the second genome. Then, pairs with common members are linked together, e.g. (A,B) + (B,C) results in (A, B, C).

ORFs may be in either orientation, and may not occur in strictly the same sequence.  The purpose of the query is only to list ORFs which are near each other in both genomes.

Example:

Distantly-related genomes should not share many conserved gene clusters. An exception to this expectation might be when fragments of the genome are laterally-transferred from one species to another. Nelson et al. (1999) had observed some conservation in gene order between the genomes of Thermotoga maritima (a bacterium) and members of the Archaea (especially Pyrococcus spp.). In the query presently explained, we can find and list these gene clusters, simply by selecting a BLASTP cutoff e-value (1.0e-10 is reasonable in this context), selecting the genomes Thermotoga maritima and Pyrococcus abyssi from the pop-up menus, and pressing Submit. The analysis yields 196 ORFs in a total of 69 clusters. In contrast, Aquifex aeolicus shares 26 ORFs in 9 clusters with P. abyssi, and E. coli K12 shares 126 ORFs in 46 clusters with P. abyssi. A "positive control", using the euryarchaeote Archaeoglobus fulgidus, yields 239 ORFs in 84 clusters. Although the Thermotoga-Pyrococcus relationship is not proven by this analysis, the clusters found can be further characterized by the researcher for other signs of lateral genetic transfer. Are the 193 Thermotoga maritima ORFs that are similarly clustered in Thermotoga and in Pyrococcus similar at the sequence level, for instance? The "Genetic mosaicism" query may help answer this question.

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