Question: Using Mummer And Deciding Which Alignment Program To Run
0
gravatar for Love
9.0 years ago by
Love100
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
2
gravatar for Vitis
9.0 years ago by
Vitis2.4k
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 993 users visited in the last hour