Hi, I am trying to generate a high quality model for GPR146 by homology modelling method ( I will use modeller) .As you know a good alignment is a very important step to get a good model. I did search for a template by BLAST, and also I used HHpred prgram. Because the strategy of my project is not to use only one search program for finding a template. When I picked one good template which was given by both of BLAST and HHpred, I looked at their alignment, ( the alignment between my target sequence and the template I choose). BLAST generated different alignment than HHpred!.
In my project I have to do some comparison between the two alignments and choose the best for my model. So my question is what is the differenc between the alignment generated by HHpred and the one generated by BLAST? and how the comparsion between them is useful for generating a high quality model?