Member Site › Forums › Rosetta 3 › Rosetta 3 – General › How to obtain alignment file for comparative modeling under Rosetta 3.1? › Reply To: How to obtain alignment file for comparative modeling under Rosetta 3.1?
I was just reading your post. If I understand you correctly I can just use any available tool to align two sequences. Every part of those two sequences with a positive alignment can be manually entered in this alignment file. For example lets say from sequence A (seqA_) AA 2:43 can be aligned with sequence B (seqB1) 12:53 and sequence A 48:62 with sequence B 56:70. Then my file should look like this:
seqA_ 2 XXXXXXXXXXXX
seqB1 12 XXXXXXXXXXXXX
seqA_ 48 YYYYYYYYYYYYYYYY
seqB1 56 YYYYYYYYYYYYYYYY
and now what the algorithm is basically doing is that it uses for the alignment the known crystal structure of sequence b and for the rest without alignment it does an ab initio prediction?
Thanks for you help.