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Assemble: a tool to construct and study RNA architectures - Message forums

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Making 2D model more readable
Submitted by Jeremy West; posted on Thursday, April 30, 2009
This might be something that can't be fixed, but I am dealing with a pretty large RNA (401 nt). I was wondering if there is another way of making the 2D model more readable besides the "magic wand" button (Reorganize helices). I have tried to use this button, but I am still seeing some clashes of helices (only one instance after clicking the button) or letters crunching really close together in the single stranded regions. Is this a algorithm problem or can it be changed in the Assemble program? Thanks for the help! Jeremy
Re: Making 2D model more readable
Submitted by french University, teaching bioinformatics. I\'m working in Pr. Eric Westhof\'s lab. I\'m interested in data integration and visualisation to improve RNA research. My personal blog.">Fabrice Jossinet; posted on Tuesday, May 05, 2009
Hi Jeremy, The "magic wand" button calls the RNAplot algorithm from the RNA Vienna package. Assemble recovers the helices coordinates to produce the new drawing. The single-strands are recalculated by Assemble since they're the flexible parts of the 2D drawing allowing you to edit it. To resolve your problem you can perhaps select one or several helices and translate/rotate/flip them yourself. Does it help? Fabrice
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