Question: Using Mummer And Deciding Which Alignment Program To Run
gravatar for Love
9.0 years ago by
Love100 wrote:

I need pairwise alignment for the specific two human sequences(10kb each) so that I can compare their similarity. There are five most commonly used programs in the MUMmer package: mummer, nucmer, promer, run-mummer1 and run-mummer3.

So which one is best? Thanks,

sequence alignment • 1.6k views
ADD COMMENTlink written 9.0 years ago by Love100
gravatar for Vitis
9.0 years ago by
New York
Vitis2.4k wrote:

I usually just go with the nucmer command and tune the parameters with multiple runs. promer is for protein alignment, and run-mummer1 and run-mummer3, I believe, are wrapper scripts to run nucmer/promer. Correct me if I'm wrong, as I have not been using it for a while.

ADD COMMENTlink written 9.0 years ago by Vitis2.4k
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