gap penalty in BWA

Victory · 11-13-2009, 11:40 AM

Hi,
I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15?
Thank you

annguyen · 01-14-2021, 06:19 AM

I think those are default penalty weights:

Gap open: cost to make gaps
Gap extension: cost to make gaps bigger

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11-13-2009, 11:40 AM	#1
Victory Member Location: Pennsylvania Join Date: Nov 2009 Posts: 13	gap penalty in BWA Hi, I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15? Thank you

01-14-2021, 06:19 AM	#2
annguyen Junior Member Location: Cambridge Join Date: Nov 2020 Posts: 3	I think those are default penalty weights: Gap open: cost to make gaps Gap extension: cost to make gaps bigger