Hello,
I want to make a lot of purely structural alignment of pairs of very short RNA
structures, from a length varying from 3 to 12 nucleotides (in every alignments
both RNA structures will have the same number of nucleotides), which are
supposed to have similar geometry. I tried to use cealign but the selection is
too short, and I don't think that resizing the windows will give me a good
alignment, super don't work because of the C alpha selection with the option
seq=0, align make sequence alignment, fit take only structures of the same size.
I really don't want to have any sequence based information in the alignment.
At the moment I didn't find a solution does anyone have one which can do the
task, just an idea will help me a lot ?
Thanks,
Alexis Delabriere
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