MPI

<p>This file contains the code for parallelization of the Wuchty algorithm in the VIenna RNA websuite 1.8.3 using MPI.</p

Vienna RNA subopt++

<p>This package contains all parts of the code necessary to run the Vienna RNA folding programs, including the modifications made to the Wuchty algorithm for optional multibranch loops, global constraints on the minimum number and length of helices, conditional chemical probing constraints, and an energy-independent lonely pairs filter.  The starting point was the Vienna RNA websuite 1.8.3.  Refer to the Vienna website  http://www.tbi.univie.ac.at/RNA/</p> <p>for the most current version fo the Vienna RNA package and also all previous versions.  Please cite Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26.</p> <p>This modified package is also available at  http://adenosine.chem.ou.edu/software.html.</p> <p>Have fun folding RNA!</p> <p> </p

Modified subopt.c

<p>This file contains code for implementing the Wuchty algorithm with helix filters, energy-independent lonely pairs, and conditional chemical probing constraints.  The starting point was the subopt.c file in the Vienna RNA websuite 1.8.3.</p

Modified RNAsubopt.c

<p>This file contains code for implementing the Wuchty algorithm with helix filters, energy-independent lonely pairs, and conditional chemical probing constraints. The starting point is from the Vienna RNA websuite 1.8.3.</p

Prog-RNAsubopt.c patch file

<p>This file identifies changes to the Prog-RNAsubopt.c file in the Vienna RNA websuite 1.8.3.</p

Alternate folds for tRNA Asp 7.

<p>(A) RNA fold for tRNA Asp 7 sequence based on phylogenetic data. Circles represent experimentally measured single strand S1 nuclease hits [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117217#pone.0117217.ref026" target="_blank">26</a>]. (B) Alternate functional RNA fold proposed in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117217#pone.0117217.ref026" target="_blank">26</a>]. The large asymmetric loop leaves nucleotides available for pairing with an Alu sequence. (C, D) The minimum free energy fold and an alternate fold from computations with S1 nuclease data as a hard single-strand constraint.</p

Flowchart diagram for initialization of parallelized RNA subopt.

<p>Flowchart diagram for initialization of parallelized RNA subopt.</p

Work Quantity by Window Size.

<p>The number of states within a given energy window increases exponentialy with window size. The sequence used is 247 nucleotides from the <i>Tetrahymena thermophila</i> group I intron crystal structure PDB ID IX8W [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117217#pone.0117217.ref033" target="_blank">33</a>]. The computations use the revised version of no lonely pairs constraint, 2004 thermodynamic parameters [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117217#pone.0117217.ref003" target="_blank">3</a>], and the Boomer supercomputer. Color legend: 5 kcal/mol, gray diamonds; 7 kcal/mol, red squares; 9 kcal/mol, green triangles; 11 kcal/mol, purple x’s; 12 kcal/mol blue asterisks; 13 kcal/mol, orange circles.</p

Pseudocode for the generation of suboptimal structures with the Wuchty algorithm.

<p>The pseudocode for the Wuchty algorithm is reproduced from the original description of the algorithm in reference [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117217#pone.0117217.ref015" target="_blank">15</a>]. P is a set of pairs i, j. S is a partial structure. σ is a stack. ∅ is an empty stack. R is a stack of partial structures. ℓ is the length of the sequence. Bold text highlights where new constraints were applied to the evaluation of a base pair.</p

Parallelization Scheme.

<p>The parallelization scheme shows direct communication between each core and the master core.</p