RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology

Abstract

As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae.

A 3′ terminal stem–loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication

“…3′SL is comprised of a 7 bp stem (nt 1299 – 1305 base-pairing with nt 1316 – 1322) and a 10 nt loop (nt 1306-1315), located just 14 nt from the 3′ end (Taufer et al ., 2008). This structure is shown schematically in Figure 1.…”

“…Since many viral RNA replication elements such as those found in plant viruses form pseudoknot structures, we used software tools that are able to predict these structures. RNA structure predictions were performed on the 3′ terminal 200 nucleotides of each segment using the RNA Virtual Laboratory (RNAVLab) platform (Taufer et al ., 2008) running programs PseudoknotsRE (Rivas and Eddy, 1999), PseudoknotsRG (Reeder and Giegerich, 2004) and NuPack (Dirks and Pierce, 2003; Dirks and Pierce, 2004). RNAVLab consistently predicts a similar stem-loop structure for each virus, in each case positioned just upstream of the 3′ end of RNA2 (Taufer et al ., 2008).…”

“…Despite our use of software that allowed for the prediction of pseudoknots, our results for NoV are similar to those of the previous analysis (Kaesberg et al ., 1990). In most cases, the predicted 3′SL structure formed a part of a larger pseudoknot structure, but prediction of the pseudoknot was not conserved for NoV or BBV (Taufer et al ., 2008). Whether the sampled 3′ termini in NoV and BBV were too short to detect pseudoknots that might be predicted to form in a longer sequence and whether pseudoknot structures play any role in viral RNA replication remains to be determined.…”

“…Whether the sampled 3′ termini in NoV and BBV were too short to detect pseudoknots that might be predicted to form in a longer sequence and whether pseudoknot structures play any role in viral RNA replication remains to be determined. Nevertheless, the predicted 3′SL element is structurally conserved among all seven nodaviruses examined, although each predicted structure is comprised of different primary sequences (Taufer et al ., 2008). …”

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce

“…In our previous work, we proposed to approach this problem using three steps: (1) cut a long RNA sequence into shorter non-overlapping chunks; (2) predict the secondary structures of each chunk individually by distributing them to different processors on a Condor grid and (3) assemble the prediction results to give the structure of the original sequence [8]. In our past effort we performed an exhaustive search for all the possible ways to cut a sequence.…”