RNA secondary structure predictions - G-U pairing

Edwin ten Dam ebtd1 at cam.ac.uk
Wed Jun 26 04:42:04 EST 1996

In article <4qp2to$6h1 at taurus.adnc.com>, noone at imnr.com (reset) wrote:

>I have been using RNAdraw from Ole Maatsura's lab to predict secondary
>structures of viral sequences. The program allows the user to allow or
>disallow G-U pairing in its calculations of structure and energy. I
>would like to know which scenario is closer to actual in vivo
>conditions. Thanks in advance!!
>Jose E. N. Gonzales
>The Immune Response Corporation
>Carlsbad, CA

Definitely include them. Although I haven't used RNAdraw (we're using Macs
here), there are numerous examples of GU basepairs in functional, tested
structures (tRNAs, rRNAs, mRNAs). Structure predictions definitely
improved when including GUs in the programs I've used.


Edwin ten Dam                  ebtd1 at cam.ac.uk
Division of Virology - University of Cambridge
Tennis Court Road,  Cambridge   CB2 1QP,  U.K.
Phone: +44 1223 336918  - Fax: +44 1223 336926

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