Breakpoint, single-cut-or-join (SCJ), and double-cut-and-join (DCJ) distance of multiple/pairwise alignment
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6.1 years ago
irhotep ▴ 10

Greetings. I am working using draft genome assembly of S. aureus (size approx 3.0 mbps), and I would like to determine whether one genome are related each against another by comparing the genome itself, not in the gene/ORF level, thus genome annotation step was omitted from my pipeline.

I performed whole-genome multiple and paiRwise synteny alignment using progressiveMauve algorithm and several distance variables were generated: breakpoint, SCJ and DSJ distance. Along with visualization of progressiveMauve itself, these variable will be sufficient to explain my genome comparison analysis.

My questions are: (1) Am I heading in the right diRection to determine the genome relation between my samples? (2) I tried to understand the meaning of each of these distances in the simplest word but I failed (I am of clinical medicine background). Are these variables (i.e. number of rearrangement events) are sufficient to explain the genome relation between my samples?

I really appreciate any help you can provide. Thank you very much.

Assembly alignment • 1.3k views

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