Reply To: How to obtain alignment file for comparative modeling under Rosetta 3.1?

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March 20, 2011 at 5:46 pm #5202
Anonymous

    Hi len,

    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.

    Max