Re: [modeller_usage] what is the correct alignment

[Karsten SUHRE <>]

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