AMBER Archive (2005)

Subject: Re: AMBER: nucgen problem

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 07 2005 - 14:27:14 CDT

G5 C A A A A T T T T G C3
C5 G T T T T A A A A C G3

I think nucgen reads and generates 5'->3', where in nature
the 5' base is opposite the 3' base of the other strand.

So your base *pairs* defined above are:

G5 C A A A A T T T T G C3
 : : :
G3 C A ................................ C5

Therefore a complementary 2nd strand in nuc.in would begin

G5 C A A ...

Bill
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