Interactive assessment of synteny and reversal distances with Cinteny
We demonstrate examples of interrogating evolutionary relatedness of genomes with the Cinteny server, using different types of queries and different setup of parameters. It can be used to visualize synteny around a single gene (or marker) (See example), to identify synteny blocks and compute reversal distance between pairs of chromosomes as well as whole genomes. In examples included below, we show an example of each type of query, demonstrating the effects of various parameters on the results.
In particular, the level of coarse-graining is varied as:
- NOAGG: no aggregation, only completely conserved regions
- INTAGG: intermediate aggregation, minimum length of synteny blocks and the maximum gap between adjacent markers set to 100kb
- DEFAGG: default aggregation, minimum length of synteny blocks set to 300 kb and the maximum gap between adjacent markers set to 1 mb
Note: The minimum number of markers is set to two and paralogs contained within the largest synteny blocks are used, unless otherwise stated.
The effects of such defined coarse-graining are demonstrated for the whole genome comparisons (see Example 1), and for X chromosomes (Example 2), for human vs. dog, and mouse vs. rat. The reversal distances are computed in each case with different level of aggregation. As can be seen from the figures, the reversal distance (referred to as RD) varies significantly in absolute terms, depending on the particular choice of parameters. On the other hand, the ratio of the distances between chimpanzee and human, and between rat and mouse genomes, for example, remains relatively constant for a reasonable range of coarse-graining parameters. Note also, that appropriate choice of coarse-graining parameters may be highly genome-specific, as illustrated in Example 1.
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