User:ElNando888/Static Cloud Labs/CL-III.Huffman

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This lab should prove very interesting for those who would like to gauge the relative predictive value of ViennaRNA 1.8.5 (EteRNA) compared to ViennaRNA 2.x, because at least 2 large changes in algorithm are localized very close spatially.

  • For one, many players will design with GAAA tetraloops, and as I mentioned somewhere else, the stability of this structure has been strongly revised down in Vienna 2.x (it is still one of the best "boosts", but no longer so amazingly powerful)
  • Secondly, the stability of multiloops has also been revised (mostly down)

This terminal multiloop supporting short stacks capped with tetraloops is bound to create the most dissimilar predictions between the two versions of the Vienna library.




ViennaRNA Comparisons

I'm going to generate comparative dotplots. Impossible to do this job manually for all designs, so I'll focus on the currently (17:51, 3 May 2013 (UTC)) top-voted ones for now.

For more information about the color-coding used below, see the discussion page about dotplots.


0.0 Probability color coding.png 1.0


ViennaRNA 1.8.5
ViennaRNA 2.1.1
 2712696 2714242 VRNA185.png  2712696 2714242 VRNA211.png
steve's huffman 3
 2712696 2794396 VRNA185.png  2712696 2794396 VRNA211.png
Huff Person

 2712696 2732683 VRNA185.png  2712696 2732683 VRNA211.png
Fiskers Huffman 3

 2712696 2713989 VRNA185.png  2712696 2713989 VRNA211.png

 2712696 2713681 VRNA185.png  2712696 2713681 VRNA211.png
The last of the Huffmen - Brourd - Lab 'Huffman' R1 - Sub 3 (Mixed Things up a little bit)

 2712696 2713651 VRNA185.png  2712696 2713651 VRNA211.png
Huff and Puff Man - Brourd - Lab 'Huffman' R1 - Sub 2 (GAAA Tetraloops)

 2712696 2717337 VRNA185.png  2712696 2717337 VRNA211.png
Mat - Huffman D1

 2712696 2771229 VRNA185.png  2712696 2771229 VRNA211.png
Huff n Puff

 2712696 2732681 VRNA185.png  2712696 2732681 VRNA211.png
Fiskers Huffman 2


And since we're comparing, one of Vinnie's designs. 


ViennaRNA 1.8.5
ViennaRNA 2.1.1
 2712696 2736768 VRNA185.png  2712696 2736768 VRNA211.png



My submitted design


Yeah, I know, it looks quite crazy...

This is an experiment related to the ideas I'm presenting in CBPP. In this specific case, I'm curious to see how the internal loop 5'-GAUGGUA--GAGAGUA-3', which is presented as a "stacked duplex with seven non-Watson Crick pairs" by the SCOR database, will show up in the SHAPE data.






Well, what do you know. That insane stack actually worked...

For the sake of documenting it, this stack comes from PDB accession 1A4D, and it looks like this:



Note that the only real canonical pairs in this stack are the top-most and the bottom GC pairs, none of the seven pairs in between are canonical (more details about it in this blog entry)

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