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Messages - jmmmggg

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RNA structures (DSSR) / Classification of helix versus loops
« on: July 06, 2023, 03:04:18 pm »
I am an undergraduate student interested in studying tetraloops.
My partner created a file using DSSR containing all hairpin loops, and now we are trying to determine which loops qualify as tetraloops.
We have some 6-nucleotide hairpin loops where it appears as if the first and last nucleotides are interacting as if they were a tetraloop, but we could not tell for sure. Thus, we are wondering what DSSR constitutes as a base pair, as well as how it defines helices versus hairpin loops.

Thank you!

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.