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[modeller_usage] what is the correct alignment

To: modeller_usage@salilab.org
Subject: [modeller_usage] what is the correct alignment
From: "rudra" <rudra@bic.boseinst.ernet.in>
Date: Thu, 16 Feb 2006 15:31:18 +0530

hi,
i'm new to homology modeling, i was trying to solve a structure by homology
modeling, i want to know what is the correct alignment among these two:

case 1:
template              abbadfaclkzcdtcfdgswchc
target                aabadaacckzcct----ccghc
secondary structure   CCCCCCCHHHHHHHHHHHHHHHH
CLUSTALW              * *** ** *** *       **

case 2:
template              abbadfaclkzcdtcfdgswchc
target                aabadaacckzcctccghc----
secondary structure   CCCCCCCHHHHHHHHHHHHHHHH
CLUSTALW              * *** ** *** **    

regards,
rudra

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