conservation analysis when only a few syntenic blocks are available

[vaquerizaslab]

conservation analysis when only a few syntenic blocks are available

[liz-is]

Hello,
I don't personally have experience using CHESS to compare between species, but it sounds like this is an ideal use case for the --background-query option, which will run comparisons between all regions of the genomes (non-syntenic), which can then be used to calculate a p-value for the similarity of your syntenic regions. @nickmachnik knows more about this, maybe he can give some more specific guidance (I'm realising now that the docs are not very detailed for this part!)

[nickmachnik]

I agree with @liz-is, if you need to put your comparison results into context of some random expectation, using the --background-query flag is an option. Your reference block will then be compared to the whole query genome, in a block size equal to the syntenic query block. Whether that is a meaningful background model depends on the goal of your analysis.

[zy041225]

I see. Thank you.