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Old 10-28-2014, 06:27 AM   #2
Sheree Yau
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Location: France

Join Date: Mar 2014
Posts: 6
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I think you answered your own question with your tests. NUCmer is faster than MEGABLAST, but perhaps less sensitive. So depending on your project, is speed more important than accuracy?

Another consideration might be whether you favour longer alignment lengths of lower identity, for example for detecting synteny. From my experience, I tend to prefer BLAST since the time is not limiting until LOTS comparisons and I find there's many tools out there that take BLAST outputs.

I also like using Artemis Comparison Tool (ACT) (http://www.sanger.ac.uk/resources/software/act/) for visualising BLAST alignments. Good luck!
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