Dear Rudra,

in the context of homology modelling, the question you ask is "which residues are structurally homologous to each other". This question cannot be answered by a pairwise sequence comparison alone. You need to build a multiple alignment using a series of homologues of your template as well as of your target. If you are dealing with a mixture of sequences and structures, T-Coffee is a good choice (see http://www.igs.cnrs-mrs.fr/Tcoffee/ for a Web-Server). However, given the fact that you have 'B' residues in your alignment, I gather that you are asking the more theoretical question of whether a GAP should be inserted in the position you show or not. But again, this question is best answered by looking at families of proteins rather than at pairwise alignments alone. If you use multiple alignment programs (or threaders) that use structure information in the process, these tools will implicitly account for arguments such as "better do not insert a gap into a secondary structure element".

I hope this helps,

Kind regards,

Karsten.

On Thursday 16 February 2006 11:01, rudra wrote: > 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