This query no longer produces a plot as described. It now lists the numerical data enabling you to produce a plot.

Remember,

To jump to this query's analysis page click on the corresponding link in the navigation bar above underneath the "All Analyses" heading.

Description of the genome query for

Genomic Dot Plots

For each ORF in the first chosen genome, all of its matches with ORFs from the second genome are identified.

The strength of each match is then plotted, where x = locus number of ORF from genome 1 and y = locus number of ORF from genome 2. The better the match, the whiter the dot.

If, due to compression of the graph (e.g., fitting 1600 loci in a space of 800 pixels), two or more matches map to the same pixel, the best match (brightest dot) is displayed.

For intragenomic dot plots, the self-matches are not displayed.

Example:

It is only worth plotting related genomes, since conservation in genome organization quickly disappears as phylogenetic distance increases. A good example of how one might use the dot plot query is to look for genomic rearrangements such as insertions/deletions, inversions, and transpositions. Performing the query on Pyrococcus abyssi vs. Pyrococcus horikoshii, for instance, reveals an assortment of rearrangements within a background of overall colinearity. The same query applied to Chlamydia trachomatis and the closely-related Chlamydia muridarum reveals very few differences in genomic organization; those genotypic differences, however, may be important in determining the phenotypic distinctiveness of these pathogens.