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Old 03-07-2011, 12:45 AM   #1
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Location: France

Join Date: Jan 2011
Posts: 5
Default Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost)

Dear Sir,

I am trying to perform global alignment for contigs to several
chromosomes in genome using Mummer.

I am wondering what is the parameter I can use for setting the parameter below
  1. Gap Extension Cost (e.g. I want to set it to < 1).
  2. Gap Opening Cost.

Specifically for "nucmer" script.

Thanks and hope to hear from you again.
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