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Hai modeller people!!!!!!!!

Dear modellers,

  I am having a doubt in homology modelling.Please help me to overcome
this problem.

I am having a template/target alignment file like this:

>P1;xxx (template alignment)
-------------------------EPTIHKLAGCTA and go on.
>P1;xxx(taget sequence to be modelled)
MTGCATDAERAEPTIGCTAADEGRAEPTIHKLAGCTA and go on.

My question is how to model the region in target sequence that doesn't
have any corresponding coordinates to get from template
sequence.(reference structure).

Kindly suggust me solution to overcome to this problem.Thanks in advance.

                                         Yours sincerely,
                                            Senthil kumar.R
  
     R.Senthil Kumar,
     Junior Research Fellow(JRF),
     c/o Dr.Akash Ranjan,
     Computational & Functional Genomics Group,
     Centre For DNA Fingerprinting & Diagnostics (CDFD),
     Hyderabad-500 076.
     
     Ph:040-7151344-Extn(Lab:1304)
                        (Hostel:2300)
     E-mail: