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

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

1.0

ViennaRNA 1.8.5 (EteRNA)	ViennaRNA 2.1.1

steve's huffman 3

Huff Person

Fiskers Huffman 3

JR_Huff_Rnd1_Sub2

The last of the Huffmen - Brourd - Lab 'Huffman' R1 - Sub 3 (Mixed Things up a little bit)

Huff and Puff Man - Brourd - Lab 'Huffman' R1 - Sub 2 (GAAA Tetraloops)

Mat - Huffman D1

Huff n Puff

Fiskers Huffman 2

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

ViennaRNA 1.8.5 (EteRNA)	ViennaRNA 2.1.1

Maordien

My submitted design

o_O

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.

Links

Results

O_O

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)