[modeller_usage] what is the correct alignment

16 Feb 2006


      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