Computational protocol: Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

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Protocol publication

[…] RNA sequences of all 10 sotRNAs and 2 intergenic ncRNAs were used for structural predictions using 5 different methods: RNAfold-MFE, which predicts the Minimum Free Energy (MFE) structure; RNAfold using thermodynamic partition function centroids algorithm; ContextFold, which uses a very large number of parameters in a machine learning approach; Vsfold5, which allow the prediction of pseudoknots by using sequential (5′ to 3′) folding and thermodynamically most-probable folding pathways and Cylofold, which simulates the 3D folding process in a coarse-grain model. All predictions are shown in extended dot-bracket format to include pseudoknots. All 5 methods were run using their respective web-server versions and default parameters. […]

Pipeline specifications

Software tools RNAfold, vsfold, CyloFold
Application RNA structure analysis
Organisms Halobacterium salinarum, Halobacterium salinarum NRC-1